Unless you make a habit of standing in front of the saddle with the bike in between your legs (thus laying your nuts down on the top tube), I'm not sure why you'd worry about it. I don't know about you, but I don't ever straddle my bike. I'm either pedaling or leaning over to one side with a foot down on the pavement, but in both cases, I'm still sitting on the saddle. I might be the odd one out on this though...

As for why top tube is important - the general wisdom is that you really shouldn't run stems shorter than 90 mm or longer than 130 mm (for various claimed reasons). While 4 cm sounds like a large range of adjustment, it's much less adjustment than you have in setting your saddle height, for instance. That's why I'm saying it's important to get that as close to spot on as possible. I think most bike dealers/fitters/riders would agree. Of course, seat tube length matters too as that usually dictates head tube length, which will in turn set a range on your saddle to bar drop (or rise).

Anyway, pay less attention to me and give John Dacey (that's his name) a call!