Typically I solder the dual pot in first and then try to set the pot on the pcb and set them in the enclosure. Tighten all the pots to the enclosure, then solder to the pcb inside the enclosure. It’s a bit finicky keeping them all lined up correctly though.
alternatively, I use pot covers (like from tayda) on all the other pots. The single pot with pot cover is roughly the height of the dual pot. Instead of the pedalpcb spacer I use foam tape, and apply it to single pots as well. Then they’re all pretty close to the same height resting on the pcb. But this doesn’t help with the top pots that hang off the pcb.
in your case you’ll have to de-solder the single pots. Or maybe try to add a nut inside so they touch the enclosure at about the same height, but idk if that would work well or have enough thread to attach.
I keep saying “roughly” or “about” regarding matching the height, since in my experience the legs of the pot will bend and give you some flexibility, but you want to avoid too much height difference (like you have currently) so you can tighten the pots without putting stress on the solder joints.
