Looking for guidance re large team designs

1) A general rule of thumb is to register the outputs of each partition(I know, it's not always possible). In general this isn't that big of a deal, but sometimes requires moving stuff around. Note that this is based off of what Incremental Compilations underlying principle is, that it saves compile time by not having to re-synthesize and possibly re-fit partitions that haven't changed. If one partition's results are dependent on another partition, then you just have to re-do everything.

2) I've never seen anyone use .sdc files for partition boundaries.

3) SignalTap comes in after the merge, which means it views the design as being flat. It works the same whether or not you have partitions.

I don't get how you would have two different entities NCO with the exact same name in a single VHDL project to begin with(you can have architectures with different configuration bindings, but it doesn't sound like what you're doing.) Heck, a bottom-up flow with .qxps would actually work since you can build Entity1 and Entity2 separately, but it still seems like changing the name would be much simpler and much less confusing in the long run(having two very different behaviours for something that has the same name seems like it could cause problems.)