Enderal SE
Hero menu attributes have been moved to DLL and rewritten using C++ API, not matching the old Papyrus methods 1:1. The race bonus I would not consider a bug because it's a permanent effect. Item effects should be green, that's an issue I'll look into.
If anyone else reading this is having this issue and are too lazy to look at their item and race bonuses and do the math (like I am) to see what their base skills are at so they don't waste pennies on learning books they don't need. I found a workaround for this issue using the following mod and its requirements.
https://www.nexusmods.com/enderalspecialedition/mods/682
Skyrim Character sheet preset for enderal se on nexus incase the link doesn't work.
I have roughly 6 hours into a save using this mod and have encountered no issues so far.