The way to run multiple Indi servers is to chain them together which is exactly what I do. I have my x64 device (an Aaeon UP Core) on the dovetail to control EFW, Cameras and focuser. A RPi2 is on the RA axis and controls the mount. Both run INDI with drivers relevant to their tasks. Note: The RPi2 runs without a GUI so it doesn't have much to do except run INDI server. The primary INDI server is on the Aaeon and I chain the RPi2 INDI server using INDI web manager remote driver option which in my case is "Avalon StarGo"@10.42.0.1 (the Pi2 runs a wifi hotspot so my Aaeon has 2 wifi devices: one to connect to the RPi2 and one for the main connection to the rest of the world)
I run Ekos on a third Windows machine and simply connect to the primary INDI server on the x64. It forwards all comms to/from the RPi2 so it looks like the RPi2 drivers are on the Aaeon. So from the main computer everything is in one place.
The only "downside" is that all work on the RPi2 is through the command line via SSH from the Aaeon.