One of my friends who's a lot in jet fighters came over last night and I confronted him with the issue. He told me that jet fighters (like other planes) have position lights but over enemy territory these are (understandably) switched off. However, to avoid collision with your other jet fighters in formation flight they have lateral, flourescent "lightsheets" that are only visible to the wingman next to you.
Of course, leaving the lights on in these rooms with "skylights" (or "spacelights") might serve the same purpose, IMHO.
As for the sensor theory I have the impression these are within the hull and indicated by the three segmented circular lines (two at the saucer's bottom stern, one at the saucer's upper bow - at least on the 'pilot' VFX models), that look like visual warning stripes to me, something along the lines of "Warning! Sensor Emitter Radiation".
I should also point out that there's a similar white and illuminated rectangle on the bow of the pilot Enterprise's
elevated bridge dome structure. Personally, I'd like to believe this one to be a panoramic window of the original circular briefing room from "Where No Man Has Gone Before" - which unfortunately we couldn't see in the episode because the camera was facing / shooting the other way.