Once you get through the screen, you can show them your fancy resume, but at that point, no one cares about your resume -- you already caught their attention and it is interview / references time.
The reasons are often somewhat complex. Their application tracking software only supports word. Their IT department has sent word from atop the mountain to only accept .docx because it works with their AV and a bad virus got into the company via PDF last year.
It isn't the people you are going to be working with that are the problem, it is the people who defend the outer ring of large companies -- IT and HR departments.
Larger companies may do this, and if you like larger companies, this is probably ok. Not for me.
But companies also have a zillion "well if they don't want to work with me I don't want them working here" rules.
Listen, sometimes in the real world you have to do something a little unpleasant every now and then. Candidates should bend a little to employers, and employers should bend a little for candidates.