I am currently pursuing an MSc and am preparing my PhD application. For this reason, I reach out to professors I know well in order to ask them whether they would be willing to write recommendation letters for me. I got a BSc from a different university and I obtained it by writing a final thesis.
My question is:
At the time of the application, I will only have written a BSc thesis and not yet the one for the MSc. Would it be considered a "red flag" if the professor who supervised my BSc thesis is not one of the three references I provide with my application?
The reasons why I hesitate to ask that professor is that even though my thesis turned out fine, I entirely interacted with one of her PhD students during the process of completing it and not with her personally (there are other professors who I know personally). Also, because she teaches at my old university and not at the one I am currently studying at, I question whether she might have lower incentives to positively recommend me.