Hello rockdue:
Good of you to share your experiences for others:
I have a few questions for anyone that has the time:
1. As mentioned, by bachelors is a B.A., would this count against me during the admission process? I had to write and present a thesis, and attend field camp, which is generally the only difference at "normal" universities. Also, would it look weird for me to apply for another masters? (Since IGP-A is MS + PhD).
BA as opposed to a BSC? I would not worry about it since your major is geology.
2. I selected "I am applying for MEXT and WILL enroll even if I am not selected", was this the incorrect choice? Obviously I'm really banking on the scholarship, but if absolutely necessary I could fund myself with my own savings/loans.
No, this is not an "incorrect choice" UNLESS you are applying for a "needs based" scholarship (MEXT scholarships are NOT "needs based"). Basically they have a certain number of scholarship recommendations (they choose you and then recommend you to MEXT- and except for every unusual circumstances, MEXT will approve as the university has already vetted you).
If you choose the MEXT scholarship ONLY
For example if they have 3 scholarship slots, and you are in the top 3, you will be accepted with scholarship. If you are number 4 they will reject you.
If you choose, "I am applying for MEXT and WILL enroll even if I am not selected"
For example if they have 3 scholarship slots, and you are in the top 3, you will be accepted with scholarship. If you are number 4 (and qualified, they will offer you a "self-funded admission". )
MEXT scholarships are chose on academic merit, not financial need.
3. I must ask, as everyone does, what are my chances? Subjective, I know, but I scoured the forums and could find very few Americans that applied or even got the MEXT scholarship to compare myself to. My potential advisor said I was the first westerner to apply to his lab, so I don't know how they view Americans.
You are may be "overthinking" - Why are there few US applicants, - in the US the education level is very high - so why go overseas…?
Culturally, the US (no offense intended) is IMO a bit egocentric, so overseas "education is not so highly sought" especially in non-English speaking environments.
I think "how they view" Americans is NOT the big issue (although it would surprise me if at least some of your interviewers had not done POST DOC in the US) - it is how they view YOU in the interview.
Team player, hard working, "research mind" & willing to learn!
Good luck