Don't be embarrassed - I was getting ready to ask a question about this as well.
Someone recently said on here that the screws on a T-O-M ought to be facing the pickups not the tail-piece.... BUT the Tokai Love Rock I bought last weekend is the first guitar I've ever had where this is the case - and it looks very odd to me!
All other guitars with T-O-Ms I own or have owned (including my current Epi LP, SG and my Gibson Explorer) all have the screws facing the tail-piece! The Epis were 2nd hand years ago, but the Explorer was brand new last month.
So my question was going to be - is there a right way?
In answer to yours, I have had no difficulty at all with setting intonation on all these guitars that have the bridge the "wrong" way round. In fact, I'm getting totally confused when I keep turning the screws the wrong way on the new Tokai.
If anything, I would say it's easier to adjust intonation if the screws are facing the tailpiece - when you need to undo the screw (so the saddle is moving away from the screw-driver), at least the saddle wants to move, the string angle behind the bridge is pushing it. With the screws facing the other way, I have to detune, and lift the string off to make sure it actually moves the amount it's meant to.
EDIT: Ah Philly Q beat me to it - good point about the strings touching the screws, I have experienced that, but not enough to upset me.
So glad there are no rules!! I'll turn my Tokai TOM over then - it's offending me! :lol: