Regarding the midi effect issue, that might be a compelling reason to use one instance per instrument track in Logic Pro, giving up some of the other advantages of multi-channel larger instances. Logicpro is the only daw that even had a proper midifx plugin section so you gotta give it credit for that but it is true then when you use a multi timbral instrument such as vepro, then all the midi for that multi timbral Instrument have to funnel through a single midifx section.
It will be much more simple to manage midifx, if you are using them, on a per channel basis rather then all channels through a single plugin.
That being said, it’s still possible to manage multiple channels through some midifx plugins if you want to use larger vepro instances, but it makes the midifx setup more complicated. Scripter, for example, can be programmed to handle each midi channel and port differently as desired, but that can result in large and complicated scripts.
You could alternatively use a tool like plogue bidule in the midifx section to split off each midi channel to a different midifx plugin chain inside plogue bidule, presuming you can do what you need to do entirely with third party midi plugins.
Just two examples. Possible, but complicated.
There are some other advanatages to using one instance per instrument track, such as easy freezing, easy audio routing, etc. It is probably the most hassle free way to go. But you also lose some of vepro’s capability since you aren’t mixing in vepro at that point.
It just depends a lot on the workflow you like to use