When this is released what will the GUI look like? Will it be massively cleaned up so users like me can edit a lot of the bot without opening files and sorting through code? Can we do things like avoid a certain strongbox because it has a specific mod we can't handle all through gui?
Keep up the good work.
Beta has been available for use as soon as this thread was made.

Just click on the Latest Download link in the second post, and you'll get the latest Beta available.
The ExilebuddyBeta User's Guide also goes over most of the basics, but a few of the images need updating. They will be updated soonish, but for the most part, all of the information there is still relevant.
As for your question, the code aspect is always going to be a main part of the project. If you want to avoid it entirely, you're going to be really limited as to what you can do and configure with what we provide. We have to take an approach of general -> specific. So, we'll make sure we have all the capabilities for people to do the things they want, but we can't specialize all of those capabilities into really polished features for end users in the short term. As time goes on, and we have less broad things to do, we'll be able to start focusing on specializing various things, but that's not going to be anytime soon for the short term.
That is where the whole user driven development aspect comes in. If people want to make things better than we have our basics setup, they'll be able to. That's been the driving focus for the Beta rewrite, to get the project setup in a way where people can actually develop meaningful things with what we provide and not be impeded by our code.
To answer your question directly, the answer would be no, you won't be able to completely configure the strongbox logic through a gui with what we provide, because what we provide right now, is the means to do those specific interactions with the strongboxes. How the bot actually does it, is dependent on the implementation used. For just showing off the feature, I added in a basic example that uses transmutations on a white strongbox, but obviously there's a lot of different things that can be done. Writing a fully complete system that was fully configurable through a gui would make for a good plugin, but on the priority list for the things to work on right now, that's pretty low.
The current critial priority list for beta is as follows:
1. Rewrite Exile into something more usable with a minimal gui.
2. Rewrite TspExplorer to fix the performance issues when exploring.
Once those two things are finished, Beta is pretty much ready for more general use and testing, and where we go from there, will be dependent on the feedback we get. Extensive strongbox features would be nice, but those only exist in one league right now, so it would be better for us to work towards general quest support, boss farming, or actual map logic before specializing a feature like that. I do foresee strongboxes becoming a standard feature of the game, like Shrines did, but we're still months away from that possibly happening.
Hopefully that makes sense as to the direction we're going in; general support first, and then specialization later.