If I am using superior characteristic augmentation to boost my agility, therefor giving me a higher dodge score due to the modifier, can I use this modified value towards a martial art or ars magnus that has a dodge requirement or are the requirements purely your base values without anything else considered besides innate bonuses?

I have always ruled it that yes, you can use based off of magical/ki/psychic/artifact boosts. However, remember that you will also need to learn while having the requirement as well, so it would take a very long time to learn with Ki Augmentation, since you can only power it for a certain amount of time.

Speaking purely by the books, yes, but you'll also need to spend the learning time necessary which, by the books, can be ages. As Nurddude points out, you can only really maintain such boosts for so long (even if you don't use the official AS policy of not being able to recover Ki while maintaining ki abilities) and, when your boost ends, you're no longer qualified for the martial art or magnus. What's more important is that you'll need to have the spare DP, MK, and/or slots for Martial Arts at the time of the boost in order to learn, which means holding yourself back from developing permanent abilities just to grab something you can only temporarily learn and use. It's an interesting idea for a character, someone who needs to power up just to use some of their abilities (very DBZ of you), but it's definitely not a very effective way to go about it.

So, to be clear, your boosted agility would count towards requirements (because it would increase your innate bonus, which always counts), though why you would want it to is anyone's guess.

Where is this rule about not being able to recover ki while maintaining a ability? The concept of the character is a martial artist who is freakishly strong and fast. With the unification of ki points rule being used and Ki Recovery 3 advantage I would be getting 1 ki every 2 turns. Superior characteristic augmentation maintenance is 1 ki every 10 turns so I had planning on boosting my dexterity, str, and agi all by 4 and maintaining them permanently. That rule would pretty much break the character concept i had planned.

Where is this rule about not being able to recover ki while maintaining a ability?

It's official errata by Anima Studios, though where exactly it's posted I'm not certain. I'm 100% certain it's not in the Web Addendums or the books, but it's from an official forum post which I believe I've seen before (though, with my headache right now, it could just be that I've seen it quoted so many times it's like having seen it).

Some people play it per that post, others don't. It's best to ask your GM how they play the game, and even if they're going to let you recover per two turns, or make you wait to recover the full amount in the minute (because the recovery every two turns is an optional rule within the optional rule of Unification of Ki).

I'll search for the official post to see if I can find it, but it may have been in the Spanish forums or, worse, the French ones, which would prevent me from doing so. Still, I'll take a look and see if I can get it straight from the horse's mouth, rather than from all the posts which quote it.

I thought it was already fixed in the Core Exxet? It was a math error, and they fixed it.

If you use Core, it works. Core Exxet, it doesn't.

EDIT:: I don't use a lot of Ki, so I don't actually know all the details.