I have a similar issue, but not exactly the same.
So far, the new M1 mini seems to 'forget' it's screen configuration and try to figure out what's happening from scratch every time it 'wakes'.
The M1 does not seem to sleep in the same way as the Intel macs - that's probably related to the issues I've been seeing.
I read through this thread, and I admit - it's frustrating to see the 'apologists' pile on and defend Apple out of the gate. Clearly, they have made some substantial changes here to this new model and it's most certainly affecting the user experience. Let's not get into 'hey - you're just holding it wrong' mode. There's a lot of complexity in monitor configuration that works, and that does not work well with this model.
My setup is I like to share the desk with 2 other machines - so I have a HDMI switcher and a power bar that senses power draw from one monitor, and when that first monitor powers up, the other one gets power from the system. It's complicated, but it typically works pretty well. What I've been finding is sometimes the Mac can manage to wake the monitor, and sometimes it can't. I happen to have another device in sleep mode on my desk, and when I toggle that, the mac finds the second monitor, and eventually then finds the first.
I also am using a lenovo thunderbolt 3 dock for one of the HDMI monitors. It's generally working really well - but the odd time this dock does need to be unplugged and plugged back in when switching things around a lot.
The reality is - this is a desktop - and users will expect it to run a myriad of configurations well and without issue.
Also - I have been running into the flickering issue after a 'sleep' cycle. Only cure for that so far is a restart.
I'm still experimenting with the sleep settings and I will re-post any work arounds for monitors and I encourage others to do the same. Thanks for sharing!