I've been using route domains (with strict isolation) paired with a dedicated partition since they first got supported.
Find them extremely useful, powerful and flexible.
As you said, main thing is to make sure you're organized on what things you want to keep under the default partition (Common) and route domain (0).
My main complaint with route domains for years has been that FQDN nodes are not compatible with them. If you create an FQDN node on a partition which already has a non-default route domain (Ex. 1) assigned to it, the dynamic IP FQDN nodes get assigned to default route domain '0'. I've opened several support cases over the years asking about it, but all responses ended up as a feature request for year 3274. Tried to accomplish the same result with iRules a few years ago, but never got anywhere.
https://community.f5.com/t5/technical-forum/ltm-fqdn-based-node-addition-with-route-domain/m-p/263694