Welcome and congrats on the GF! I jumped right in and skipped all the tutorials etc when I got my GF too, but that method does mean you are going to go through a lot of practice material trying to figure out the stuff you can learn pretty quickly by reading up on all the tutorial projects you posted.
This link is invaluable to understanding what all the manual setting do and it’s my favorite it of info. It can really help you understand how setting work and what they do.
This has a lot of good info too.
About the question of the GF changing setting based on file format; No, it doesn’t. The settings that are pre-programed for proofgrade material (PG) are based on material, not file types.
About the acrylic. If you are asking about the frosted look that you got with acrylic, that’s exactly how it’s suppose to work. Clear acrylic will turn white/frosted when engraved. There area two types of acrylic called cast and extruded. Cast engraves more opaque white and extruded engraves more clear, but it’s still at least slightly frosted. As far as masking goes, you don’t have to mask acrylic becasue the general purpose of the masking is to keep the smoke/soot from staining the material and that’s not an issue with acrylic. (Masking does have other uses though and can prevent “flashback” on the back of the acrylic.) If you had white hazing/blemishes on the edges of your cut acrylic it’s a setting issue. There’s been a ton of discussion about acrylic that you can find with a search.
Example of cast acrylic engraving.
The deeper you engrave it, the more white/opaque it tends to go.
Oh, a couple of little things. We usually call the Glowforge user interface the “GUI”. (That’s the thing you upload your project to and I think that’s what you meant by the Glowforge app. )
Secondly, you triggered my OCD with the random placement of the files on your materiel lol. 
I obsessively try to pack all my designs as close together as possible becasue I want to eeek out every inch of my material. (I’m just teasing you BTW, there’s absolutely nothing wrong with how you did it.)