If you hand a deck to a laymen and ask them to shuffle they're probably not going to do an in the hands riffle shuffle or a perfect faro either, but that doesn't mean that when you do those things they're going to think 'I wouldn't shuffle like that, he must be doing something sneaky'.
In the same way they don't think something's up just because you flipped the pack over a different way to them. It's not like you are flipping the pack over in a particularly elaborate or suspicious way, you simply flip it over sideways rather than lengthways. It's a perfectly reasonable thing to do.
People seriously don't care about this type of stuff, because they expect the magician to handle a pack of cards different to them. As long as you don't stiffen up and start acting awkwardly when you do the sleights, these moves seem perfectly natural.
Tom