When it comes to speculating on the stairs and possible room above Professor Elm's Lab, there are a few things we can rule out. For instance, it couldn't be the location where we choose our starter as in the scans it was shown we obtain them on the lower floor. Also, it couldn't be where the Heal Machine is either as that is also found on the lower floor of the lab also. Now as for it being his home, we may or may cross this out as it really depends. Now that we have a supporting role for the unchosen gender, either Prof. Elm's house can be used for them or one of the unimportant houses located in New Bark Town can be the housing of the new supporting role. So, the idea of it being Prof. Elm's house is still questionable.
There are a lot of aspects for this second floor. However, seeing as not much emphasis is being put into it, I do agree that it just may be somethign minor. Although, it may not have been mentioned heavily as yet as it could be a larger secret for after the main game's plot. I guess really, it is one of those large questions the fans have at the moment until something is told or unless we play the games ourselves. I wouldn't be surprised however if it was added in for design, but we can't tell as yet. Oh yes, I forgot that there is also the possibility of it being the solid idea of how Silver steals one fo the starters, which I think is the most probable for right now seeing as it agrees with what was placed in the manga.