Export for screen PDF default settings size is bigger then if manually and take a very long time

Hey, so I've got a few pdfs with no bitmaps at all, just vectors, 12 in number. I need to apply a series of changes to them and then save them back in a Illustrator Default pdf format. I started doing them 1 by 1 in and saving them back, all ok no problem saving was almost instantly. Then I thought I should make an .ai with all of them on each artboard, do the changes 1 time and will affect all, then use the Export for Screen/PDF (set to Illustrator Default) feature and export them. 

The problem is Illustrator then freezes and the export take a long long time, talking about 1 appearing in the folder after around 3-5 minutes, while if I were to export them manualy this would been almost instant. 

I also noticed the size is different (from 2.5mb to 13mb) even tho I used the same pdf presset (Illustrator Default). Can anyone explain to me why is this happening ? Thanks !