TheGigRig has a deserved rep for pro pedalboard solutions. Its new QuarterMaster is a neat strip of separate loops that gives you independent true-bypass switching over whatever is in each.
That could be as simple as keeping problematic pedals completely out of your signal chain when you're not using them, or you could set up separate groups of pedals in single loops to suit your needs.
The QuarterMaster is available in various configurations; we have the six-loop option (£169), but see TheGigRig's website for other sizes and custom orders.
The relay switching and bright blue status LEDs require a nine-volt mains supply with a Boss-style adaptor. There's a bracket kit (£6) for Pedaltrain 'boards; we'd opt for a rubber pad (or Velcro) and cable ties for anything else.
We used the QM6 for a recent Dunlop Fuzz Face comparison video, and it coped admirably: no ground loop hum, no pops and bangs, just reliable, instant switching.
In another setup, we assembled a main, everyday collection of drives, modulation and delay using four loops, but had two completely separate chains of pedals on the remaining two loops - one broadly Hendrix-inspired, the other slightly harder rock.
Those extra loops would cause all sorts of issues were they all in one great big line - here, the segregation means it's more like having three small pedalboards in one, with no problems.