You are correct, I should have reported that
my car is an '04 330Ci, so we probably have the same engine/pan combo.
I'm sure another 4000 miles with a small amount of the old oil will make no practical difference. I'd just wait till you do it again.
Next time just be positive that you hear the sucking when the tube is touching oil pan bottom.
And of course pull the filter before you pump.
Yes, I do take off the refill cap before pumping, but I'd bet that it is not of consequence for the discrepancy that you uncovered.