Those who have a undergrad degree from a Japanese Uni,
 

Before I get to my question, I want to say that I'm serious about attending a university in Japan. I'm currently a high schooler, have been to Japan 3 times and am planning to go again next summer on a 6 week exchange. I'm also Japanese-American. So with that out of the way...

Do you think it's worth it to go to a year of intensive language training and apply to a normal university rather than applying to one of those international programs like Waseda's SILS, Sophia's FLA, ICU, etc.?

You're sort of in the same boat as me, thinking this stuff over can be really hard.
I have a feeling though that it might be easier for us foreigners to just enroll into a international school/
Think of this, you will be able to speak Japanese in a year, no doubt about it.
But will it be nearly enough for you to fluently converse in class?
And will you be able to read at the same speed as your fellow students?

I think that if you'd enroll in a genuine Japanese only school that you would have a whole lot of trouble just keeping up.