As someone who screens a bunch of applications, absolutely I'll factor in a cover letter.

For me, the presence of a cover letter with half an attempt at customisation to the company and job ad demonstrates they actually care at least a little about this role at this company. And if it's well written then that demonstrates communication skills which I value highly in my colleagues.

It's really not often clear cut which one of two CVs is the "best qualified". The cover letter is just a bit more signal that will often swing my decision towards "let's take a punt".