3 Versions ago worked well with Passive SkillTree however recent updates made the two incompatible, my modpack relies heavily on these two and I'm curious on some kind of work around?

If you're in Shadow's discord, you can try out this unreleased build of PST that may be compatible with the latest Apotheosis. But as it stands, the issue is on PST's end, and there are no workarounds that are published publicly at least.

https://discord.com/channels/613010559532531713/613010559532531719/1259022320110931979

Latest PST update should fix this.