#1
progress as I'm learning about music theory? I often read articles on this site and such, but I'd say about 99% of them (obviously) are written for standard tuning. I'm somewhat of a newbie when it comes to theory, so would it be wise to stick with standard tuning while I'm learning?

I ask this because I'd like to be able to write songs in a lower tuning, but might get thrown off. Like if I were to play the shape of a D chord on a guitar that isn't standard tuning, it wouldn't exactly be a 'D' right? Is there some easy tip to kind of learn along with these lessons while in a different tuning? Sorry if this seems like a dumb question.
#2
It would be a lot easier most likely. If you intimately knew the notes in another tuning it would be fine but you probably don't since you just started theory. I'd say stick with standard until you have a decent grasp on theory.

Yes if you played a D shape open chord in another tuning it would be different.