Well, Bruce is introverted to the extreme and Clark is extroverted, so Clark is really not going to have problems with Bruce being there plus Bruce seem to only express his uncomfortableness in his head most of the time.
"But you're right it's very annoying having someone unannounced in your room, I hate it when my parents/brother/cousins go in and and create awkward moments because they won't leave and just watch me doing stuff or start asking inane questions."
Yeah, my parents comes in so suddenly. Mom relishes the fact that the lock is broken and she can open and close the door anytime she pleases. Usually, they come in for inane purposes like spare changes of clothes they keep in my room for some reason or to borrow my deodorant or cologne (when they are running out of the stuff) and most of the time won't leave until I tell them to. My younger sister is much worse, she comes in and demands for me to get up from my throne so she can play on my comp, last week she broke my head phones and I can't watch any cartoons because of no sound.