The tucking in of the undershirt into the underwear is pretty common... It keeps the undershirt from riding up and looking messy when worn under a dress shirt (and dress shirts look much much better when worn with an undershirt)
The penis question - don't know - never noticed and never asked...
I have to ask how long you've been married- It sounds like you're a newlywed and just getting to know each other's endearing quirks...
When I opened this thread- I had a flashback to an old All in the Family episode with Archie and Meathead arguing the finer points of getting dressed and is it sock sock shoe shoe or sock shoe sock shoe- I was expecting this thread to be similar