The manual wheel should move the needle the exact same total distance as it moves when stitching. There would need to be some pretty interesting mechanism to keep it in time if it's otherwise. However if it's like my HQ, it normally stops a bit past the highest point as that is where you need to be to have the top thread fully released from the bobbin hook. So every time the needle stops, I can move it to a higher position, but that is it's full travel when sewing.
Changing the needle height will mess up your timing. It's not that hard to do as there is normally a set screw you can release to adjust the needle height. However - you do this to line it up with the hook at it's lowest point, otherwise the hook won't grab the top thread and you'll have skipped stitches. Sometimes this is a "weakest link" part so that if you hit something really hard the needle bar may slip instead of something bending.
I have a bowl (glide) foot for my machine that will allow me to move over thick seams without anything catching. It does limit visibility somewhat even though it's clear plastic. But is sure is nice not having the foot catch on bulky seams.