It's funny even without patches I've never had issues with this scene. It's all in HOW you fly. You need to approach from the left side of the mall - fly up, then fly right, then fly down - exiting on the right side towards the arcade.
They will NOT hit you if you do not stop moving. This is at cycles of about 9000? Without patches it never gives me grief.
Just because You haven't encountered that problem, does not mean the problem does not exist. Quest games are known for their timer issues. I've played SQ4 back on a 486 [or even 386 i believe], and played the game a lot of times, through all the hardware upgrades [Pentiums and all]. And on 'newer' computers i had those issues, I had to play around with game speed and mo'slo, until DosBOX came out. Yet still, finding the right ammount of cycles is tricky.
I'll take SQ1 as an example, it has the same engine, and the same timer issues.
WIth cycles=3000 on core=dynamic, in the scene where you flee your ship, and pass a room with a few monitors showing a green Sarien face talking [the screen between the lift and the airlock entrance], the guards would shoot You when You're about halfway the screen. On cycles=4000 You'd get shot when You're about 3/4 of the screen. After playing that screen a few times, the solution was to use cycles=4000 and push game speed in the options to the max.
I bet it would be easier on another core setting though.
Anyhow, as an SQ player since 1992 or so, i can guarantee, times issues exist. ;)