This is not a fseq issue, it's a zcpp issue and I'm trying to get Dave and Keith to fix it.
With zcpp, xLights will ONLY allocate channels for the stuff physically connected to the F16. If you only have 100 pixels total connected to port 1, then xLights allocates 300 channels and that's all thats in the fseq. If you then connect 100 pixels to port 2, xLights then allocates another 300 channels and you have to rebuild everything. There is currently no way with zcpp to say "this F16 will require 16K channels sent to it, reserve that". Also it's very specific in that it chains from one model to another across the entire controller leaving no channels "free". You cannot say "I'm not using port 2 right now, leave 300 channels there just in case". All the used channels are compressed down. If you then decide to use port 2 for something, you configure it in xLights and zcpp allocates new channels and you have to rebuild everything. Basically, you WILL need to learn how to use batch render a LOT right now.
By the time this gets released, I hope to have some of it fixed. With the FPP 2.0 release, I haven't had much time to dig into the zcpp stuff. However, before it is implemented in FPP, it's going to have to have several changes. The configuration part is way to restrictive of a protocol for any real world use. Thus, there HAS to be a way to bypass that part of the protocol and use real configurations.