See
http://www.concrete5.org/documentation/how-tos/developers/third-par...

Generally, if you adhere to the license conditions, then you don't need permission from the 3rd party developer (unless that is one of the license conditions).

Bootstrap is MIT licensed, so you can use it and bundle it how you like.
https://github.com/twbs/bootstrap/blob/master/LICENSE...

While on the subject of marketplace submissions, a new howto:
http://www.concrete5.org/documentation/how-tos/developers/get-an-ad...

There are a number of bootstrap themes in the marketplace. When you create yours, just make sure to keep the original credits intact.

Any time you use 3rd party scripts (php, javascript, or whatever else), you should check the license on it first. The "safest" one to use is MIT, since that allows for commercial use.

Either way, the review board will let you know if there is an issue with any licenses during the review process of your theme.

Thanks!