Your memory is faulty. It was stated in the pilot that Kosh's ship
took roughly 4 days to travel via hyperspace to B5. That's from Vorlon
space; we don't know where the fleet was when it entered jump. Because
such ships can make their own jump points, it could've been a lot closer
to B5 space when it went in. (And was.)

RE: your other point...it's not normally expected in the course of an
average day that an invading fleet is going to come through; and in the
course of the series, that's NOT a common problem. Troops Attacking The
Station is too easy a story. What the gate is set up to do is recognize
the energy signature/coded frequency of an incoming ship or ships. It
doesn't determine the size of the ship until it's about to come out, and
thus adjust the placement of the gate sections accordingly. If there were
a war on, the allowable frequencies and codes would be changed regularly
to prevent this problem.

jms