I’am mixing manual config with director sometimes. I don’t have any problems with that at all. Which problems are you expecting? I think its not very usable, if you have more manual configured items than inside the Director, but I migrated a 100% manual config step by step into the director without major problems. Most problems are coming if you migrate things that a nessesary for a valid config, but you can’t remove them, before adding them into the director. But thats nothing what is easy to resolve.
Of course, on a paper i would not recommend to mix them, becaues its not perfect, but i don’t see any problems. If i have a handcrafted Icinga2 Checkcommand config file that another community member has build (thanks for that :)) I’am sometimes to lazy to import it into director. So why not just place it in zones.conf. What i would not recommend (outside the migrationphase) is to place Hosts in manual config. First there is no reason (that i can think of), because they are very fast and easy migrated, second, its anoying not to find the hosts in the director for fast changing. Also i think you could get duplicates on autoimport things.