You can make Smartlists for syncing, which you can make as smart as you want to select the content you want to sync over.
Yep, this is what I do- my music player mounts as two drives, even, so I have added a boolean field to the tags for whether they get synced to its external storage, or defaults to internal.
I also have a "donotsync" tag for stuff that doesn't need to go on my music player- like when I have multiple masters of an album, and don't need all of them in my pocket.
This makes it relatively easy to manage stuff going to the right place, and giving me a mechanism for reducing what will get synced when space is tight. The fact that 400GB microSDXC cards are a lot cheaper than they were is helpful though
(Sadly, MC 23 seems to have some issues syncing with my Android 8.xx Pixel 2 in the way it used to sync with my 7.xx Nexus 6, though- so I have to use external software to sync my AAC transcodes onto the phone, and can't be smart without wasting a lot of resources by making a separately pre-filtered transcode directory specifically for this device, which is a bummer.)