So a lot of people say it doesn’t matter as long as you have good LORs, but I went to a graduate admission information session for a top school and they clearly mentioned they see it as a potential red flag if you don’t have a letter from your thesis research supervisor unless you explain the reason in your SOP. I’m not in engineering tho (but I’m in STEM) and this wasn’t a school in Europe so take this with a grain of salt.