Isn't that why you do the collimation thing? To line the mirrors up?
Ideally your primary mirror cell should be square within the mirror 'box' (round as it is on the Lightbridge) and the focuser should be 'square to the secondary cage and the truss tubes fitted so that the mirror box and secondary cage go together square, or near enough.
This is one of the things I love about telescopes - while things need to be ultra precise to work at their best, there is an amazing amount of error margins built into them!
This is why we allow all that movement for the adjustment of the two mirrors and the focuser goes in and out - it doesn't matter if things are not super precise, we've allowed all this adjustment room in there.
Of course, if you do make it precise as possible you'll find that set up time is less, because you've got less adjusting to do each time.
So in my opinion, no, it doesn't matter if things are out a wee bit at all.