The latter route does seem cleaner, but as you note it doesn’t use the H90’s IO to the full potential.

If you want to set up the H90 on two location in the switcher, I think you’ll find that using Dual mode is actually more flexible and has less room for error. Using Insert mode will require you to manage latency compensation and dry/wet/bypass routing across multiple loops on the switcher, which will be painful.  Dual mode lets you treat the H90 as two separate pedals.

The best advice I can give is to take your first setup and systematically remove or bypass components until the sound improves. That will let you track down the specific interaction/route that is causing the problem.

“Best” routing method in a complex setup like this is going to be strongly dependent on your specific taste and needs.