Unofficial Fallout 4 Patch

(2) and (3) are invalid.
On average, settlers' armors and weapons will become slightly better at higher levels, but the chance for this to happen is low, due to the way the leveled lists are set up. Overall, chances are higher for settlers with a guard preference (i.e. the settlers that are created from the WorkshopNPCGuard actor base; WorkshopParentScript randomly selects from WorkshopNPC and WorkshopNPCGuard when it creates a settler). The leveled lists for the settlers' armors and weapons are still vanilla and have never been changed, so the situation can't have been any different in the past. Maybe you were using a mod such as BetterSettlers in an earlier playthrough and forgot about it ?
Same for the minutemen: the leveled lists controlling their weapons and outfits are still vanilla and haven't been changed. They ARE hopelessly underarmed in most fights, but that's a matter of game design. Note that minuetemen do not appear in random encounters, except for the late game chokepoint defense quests (though these will only occur if you conquered the Institute with the minutemen). It's also not a problem at the Castle, because these minutemen are essentially workshop NPCs (they run a WorkshopNPCScript and have been added to the workshop), so they are protected like all other settlers.
The followers' default weapons do not level. They also are not particularly powerful and they are special in only one regard: they will not consume any ammo. If followers find better weapons, they'll pick them up, but they won't use them for long because they usually run out of ammo soon. The criterion used by the game to discern which weapon is bestThe reaso is apparently not the damage but the value. Therefore, they have a preference to pick up legendary items, even if they are less powerful than their default weapons. If Preston had a pipe weapon equipped, it was almost certainly a legendary version, and he must have picked id up from a dead enemy - because the followers' inventories have never been changed, neither by us nor by an official patch.

Only (1) is a valid issue:
The cause for this behaviour is the caravan guard outfit which contains two leg armor pieces (left leg and right leg) and an underarmor item that occupies the slots for the leg armors. Thus, the leg armor pieces and the underarmor cannot be equipped at the same time, and this apparently can result in the actors being "naked" (i.e. they won't equip the underarmor). Fixing this is pretty simple, but it should be mentioned nonetheless that some aspects of this bug are quite mysterious because some people's games are not affected by this bug (myself included: I had not had this happen in any of my playthroughs).
We do not know in which order the items listed in an outfit are equipped. Assuming that they are equipped randomly. one should expect that the actors using that outfit are randomly affected too (i.e. that some actors equip the underarmor while others equip the leg armors instead), but this is not the case: they all are either naked or not. This observation suggests that the outfit items are equipped in a particluar order, but in that case, the bug should occur either always or never (because the last item equipped in the leg armor slot wins) - but this is obviously not the case either. Thus, something's fishy here.

My personal suspicion is that the bug may be triggered by a mod conflict: a mod alters the outfit in some way, which results in the items being equipped in a different order. Anyway - even in that case it's still a bug and we'll fix it.

EDIT: I'll provide a retro script that updates the caravan guards' outfits at run time. Though, for all other actors using this outfit, this fix is not retroactive.

Thank you for looking into this! (2) and (3): I was not sure about this.
But one comment: There are Minutemen in the game outside the checkpoints and they do appear in random encounters quite regularly. There are at least two locations where NPCs named 'Minutemen' and wearing the outfit spawn, and fight against monsters, just as they do after solving the main quest. This happens long before the Brotherhood appears in force. Also there is the group of Minutemen who appear with Preston to retake the Castle. Both groups are not protected and can die. Later at the Castle all the Minutemen are protected like the rest of the settlers too.

To (1): I find it interesting that you never saw the problem with the guards! I saw it in every play through, and I had quite a few. Also I never use and used mods, except UFO4P! The only exception is one mod which should accelerate loading (it works by changing the frame rate during cell loading), and a mod which introduces an item to fix a permanent change, which happens because of a bug (negative effects on stats which never go away). The latter I used just in the last play through, because I needed it, and it should not fiddle with equipment. Other mods which change appearance I never used, and also I do not 'try' mods and remove them later, or anything like that. The Faster Loading Mod does absolutely nothing with the games scripts and changes no game data at all, it just uses a special DLL to recognize loading and then uses the driver to change the frame rate during loading. I tried this for a while, but do not use it now.

So - why did you never see the problem, and I (and others) do? Maybe it is just something specific which we do differently at the start? So a mod conflict is not possible in my case. I just now use a few of Bethesda's payed mods, but this is the first time, all my other (earlier) games were completely without mods! I also start completely new every time, I do not re-use an old save at an early point. I completely delete all my saves and start a new game. So the only difference is the game version at this point and the version of UFO4P, but UFO4P cannot be responsible, because I saw the problem the first time I played, completely without mods and without UFO4P.

A point to investigate: The guards of Doc Weathers are 'naked' nearly every time. Other merchant guards are not 'naked', but Doc Weathers guards are naked nearly every time. They most often show up at County Crossing, if you have the settlement and the Caravan Station, but you can meet them nearly everywhere. It may be that only the 'Bunker Hill' group of traveling merchants has this bug for some reason, but with Doc Weathers it is nearly sure. I do not remember seeing Lucas Millers guards naked, and Lucas is one of the first you meet in Tenpines Bluff, since this seems to be always the first settlement you will be sent to, at least for me it was.