The Met clearly didn't dismiss the possibility out of hand, borne out by the references to previous local burglaries in the vicinity & the re-questioning of 3 locals who presumably had criminal records for such offences. IIRC a burglary gone wrong was also suggested by the UK police officers to the PJ quite early on in the first investigation.
IMO there would have been a few steps prior to Madeleine having to make that choice.
Assuming that she was both disturbed & frightened by a noise at the window, I think she would have first called out for her parents. When they failed to respond, the next step would be to go to the lounge & their bedroom. Only after discovering that neither Kate nor Gerry were in the apartment would she have had to choose which door to exit if she was intent on seeking them out. Was her decision made with a fearful or calm mind?
The front door was the easiest for Madeleine to access as it wasn't covered by a long curtain but it also led in the direction of the disturbance & darkness.
It is difficult to say. It may depend on whether she was woken up immediately, or there was a delay. Assuming the burglar (and as you say this is based on the OG theory) saw the cots and, presumably, the sleeping children it is plausible that they would abort the attempt to break in.
There is no certainty MBM woke immediately or, really, realsied what had happened. If there was a delay or the breeze/cold woke her then would it be obvious to 4 year old what had happened?
As Alice said it is not too easy to see into the mind of a 4 year old and understand how they may perceive events, or how they may decide to act.
Overall, I'm not sure it is certain there would have been 'flight' response - she may have simply been confused, especially if there was a delay before she woke up.
In this situation the front door seems as good a choice as any other - ultimately the choice may have been fairly arbitrary.