Yes it matters how much boost pressure you lose. Imagine you earn X amount of money, and the IRS taxes you. Now does it matter how much the IRS tax you?
Another example, if your compressor outputs 10psi but the inefficient IC loses 2 psi, so you only get 8 psi out. Now imagine a more efficient IC that loses .5 psi, so you get 9.5psi. The inefficient one nets you 20% loss while the more efficient one nets you 5% loss. This translate to how much power you make.
Now you can counter this argument by say turn up the boost even more. But look @ the compressor map. Sometimes turning up the boost shifts the compressor into a more inefficient opline. And the situation snowballs from there.
Why put more work than what's necessary? If you can get 100% of what you put in or as close to it and get it cooler and denser, than isn't that better than get it really cool and dense, but you lose 50% of it?