So I have been running with 3 instances of the Maker API all pointing to the same Node-RED server. I have an instance for all my Zigbee devices, one for Z-Wave devices and one for combo group stuff (which was the original instance).
Originally I did this was to reduce maker spamming potential and to hopefully isolate a misbehaving device so it wouldn't take down all the communication to/from NR.
I am wondering if having separate instances like this actually helps anything or just adds overhead. I've been running this way for a while and it all seems to be working well - no problems to report.
I've overloaded makerapi on a few occasions, it typically happens when I'm changing the default LED colour of all of my Inovelli lights. Even if I had everything all separated like you, I'd still run up against the same wall. I can't think of a time where I'd be sending enough commands to different communication protocols that it would be enough to overload it, so I'd say you are likely safe to combine into a single instance.
Once francois puts command node event throttling in the command node (next release most likely), it will be even less useful to have multiple maker api instances - I would think.