This is semi-intended for homour... but still a semi-serious question. Obviously the Enterprise flies over the top of V'Ger and approaches from its rear end, is tractored inside, doesn't go anywhere, and then moves forward into the "central brain complex"... which was the very next room from the rear entrance. In its ass, in other words. What gives?
Shatner explains it for us. V'Ger was modified by the Borg, and everyone knows how arrogant they are. Their own heads are shoved so far up their asses it's a surprise they don't choke on their own dung.
The Enterprise approached V'ger from behind, flew out in front of it, and was sucked into the maw there. The room where Voyager rested was in the sphere near its tail end, but more its spleen than its ass. Note the spherical part. Note the transformation effect radiating out from this section.
I can't believe we're having such an involved discussion into "where things entered" and "entered in the rear" when discussing TMP. Must be the middle of winter or something.