So, as someone who's masters thesis was around race engine design, I would like to say, you have no idea WTF you are talking about. This sounds almost exactly to me what the kids would tell me when I quized them on engine design (I taught Auto Design Series (undergraduate level)), and they didnt know/understand and were BSing an answer to me.
The pulsing of turbos makes things worse? If you were one of hte students, I would ask two questions... elaborate on pulsing, followed by what do you mean by worse? (to see how deep I could get you to go before admitting you didnt really know)
Let's get to your next point, x-pipe location and effect on scavenging (big hint word there for you). Yes the closer the xpipe to the engine exit, the increased effect on scavenging, but please tell me, in detail, how this would result in a 'back feed' in air to the turbo to the extent it causes "BIG problems" for the engine?
Point blank: A non-optimized x-pipe location (or the use of one vs not) does have an effect on volumetric efficiency, per rpm, (which I would guestimate no more than +/-5-10% range) but to suggest it will cause engine failure/malfunction, is just silly.