I’m not familiar with D&D and its class system (beyond some adaptations to PC, such as BG)
For my P&P RPGs (back when I had time for them…) I also preferred classless systems. However, I wouldn’t compare PP’s class system to that of an RPG. PP’s class system is not about character development, it’s a tool for managing the skills sandbox, to enable the creation of very distinct builds that suit the player’s style.
IMO, the OP holes don’t happen because of multiclassing - they can easily arise within one class (see 100% stealth, electric reinforcement, infiltrator’s damage buffs, faster than light travel with dash with high speed and light armor) - , but because of buffs/effects stacking, AP refunds and skills that allow to do damage without AP cost (now mostly gone, after the last nerf patch).
So as not to go off topic, you can check this thread I started on the subject. A proposal on how to rebalance skills