Alignments should be at least as accurate as they would be for male/female joints, and in some cases, even greater accuracy is called for.
Many moulders deliberately have the spindles at 89 degrees or so, rather than 90, to the feed direction. The idea is to keep (very gently) pulling the wood back into the fence. This is not appropriate for sawing, and especially not for thin-kerf sawing. The closer to 90 the better (see more)
Don't have two feedpath controls that can fight each other. For example, a fence should end where a grooved bed-plate and hold-down take over.
Bad drying and other grade issues can make the outfeed end very difficult to control. If it is not controlled, there can, at the least, be very bad back-cutting, and frequently worse. (see more)
Don't stop the wood on the sawblades. They will burn up, but actually, they are not quite as vulnerable to this as cutterheads are.
WOOD
FEED
Back-Cutting
Cutting
You MUST NOT let go of the wood until it passes this line!

Don't let go of the wood while it is still on the sawblades. It must be firmly held in all three directions: vertical, horizontal and axial.

Machine alignment for thin-kerf saws is very demanding.