I've made a mod that fixes nearly all perk issues in the game. I've attached a stripped-down version which only contains changes that are suited for inclusion in the Unofficial Patch.
Link to Nexus page:
https://www.nexusmods.com/starfield/mods/5660?tab=posts&BH=0
Changelog for the attached plugin:
Armor Penetration: Now works for melee weapons (excluding unarmed attacks.)
Automated Weapon Systems: Appears to work for all weapons even though it's only supposed to work for turrets. Added the missing condition.
Concealment: No longer overrides the magazine perks from Va'ruun scriptures or interferes with Void Form. Void Form, Concealment and Chameleon will seamlessly switch between their effects, with Void Form taking priority. (Note: Chameleon is probably not supposed to stack with itself, but the players love it. I can provide a fix if you want to risk the ire of the playerbase.)
Lasers: No longer affects particle weapons. (Expect complaints.)
Leadership: Fixed a bug that caused ranks 2-4 to only provide +15% companion affinity gain instead of +25%. Companion quests will also trigger properly. (The multiplier somehow affected the binary flags in the records under Condition Forms, so instead of getting a value of 1 they'd be at 1.15, and the conditions only checked if the value was Equal To 1. The fix sets the comparisons to Greater Than or Equal To.)
Martial Arts: Now properly adds a flat +15% crit chance to unarmed attacks instead of multiplying your base 5% crit chance by 1.15. Ranks 3-4 also have a 15% chance to disarm as intended. (Was 5%)
Particle Beams: Now properly adds a flat +5% crit chance, instead of multiplying your base 5% crit chance by 1.05.
Pistol Certification: Now properly adds a flat +25% crit chance for 5 seconds after killing an enemy, instead of multiplying your base 5% crit chance by 1.25.
Rapid Reloading: Now works while throwables are equipped.
Rejuvenation: Fixed health regeneration in combat not working. Ranks 3 and 4 now allow you to regenerate health half as fast in combat, which is what the developers intended. (Both rank 3 and 4 should use a value of 0.5 for the secondary effect, seeing as it is a combat-only multiplier rather than a separate heal rate.)
Shield Systems: Can no longer increase shields beyond the intended amount. (The bug where it reduces shields is still present, see the sticky post on Skill Fixes for a comprehensive explanation!)
Targeting: Fixed a bug that made the increased weapon range not take effect at rank 3 only.
Targeting Control Systems: Now properly adds a flat +10% crit chance at rank 4. (Rank 3 already did.)
Gunslinger's Guide and Mining Monthly magazine perks no longer count toward the skill total for the Combat tree.

Attached Files:
SkillFixes - Unofficial Patch.7z