The Thresholds are a prerequisite for Extreme mutations in their category, true. Though the one-threshold-per-character requirement does impose exclusivity, they’re NOT designed with the intent of limiting player options, and MUTCAT_MARLOSS won’t crowd out previous mutations.
(The lore involved means that it might not get along well with standard mutagens.)
I can understand the drive to make bionics not-so-compatible with mutations, though that’s not a particularly high priority for me and I think DDA works well enough without it.
When in doubt, the PC needs to be an omni-being because xe ultimately is on xyr own. If there were NPCs who could share the load (they can’t ATM), then yeah, skill caps might be a Thing and limiting character development as you describe could work. As it is, I remember GearHead2, where “interesting choices” meant “Hope you built your character around One Hobby Skill, tops, and you’ll need to start a whole new character if you want to try out something else!”
I really didn’t like that aspect of GearHead2. Would rather not recreate it in DDA. Thanks.