I see what you're asking. A lot of the factory patches with amp sims are 4-effects, but I found a handful of factory patches that had Amp models along with Cab sims in them and with 5-full effects in the patch. I had no Overflow Error when changing the factory Amp sim in the patch to ANY of the other amp sims.
However, as an experiment to test my "cumulative" theory - I started filling up an empty slot with mutiple instances of HD Hall (high definition Reverb effect that uses almost 30% CPU power). After about the 3 or 4th instance of the HD Hall effect, the unit could not add another instance of HD Hall. Instead, displayed the "Process Overflow Change Effect".
For those like me (who've not had a B3n or seen this message before), it essentially means hey dummy, you've used too much CPU power with your doomsday patch of awesomeness, how about selecting a lighter effect - can I interest you in a nice tremolo effect perhaps?
You can still cycle through the effects looking for a "lighter" one that the B1-Four will allow you to use. It will tell you which ones can be added with the remaining memory left because the error message goes away from the screen when you land on an effect that can still be added with whatever amount of memory is free. That said, I've yet to encounter the Process Overflow message while building my own patches.
So I guess the answer is a little bit of both - I guess technically, the Amp sims are all 1-slot, but it really is all about the cumulative stacking of which exact effects and how much CPU all of them use.