That could be an issue, if people do not pay the commissions, and legal stuff to worry about.
Yes, the stuff should take some actions manually (contact the seller, may be accept the payment manually, suspend the seller in extreme case, etc) if the invoice was overdue. But don't think it's a big problem. If seller created products, posted them and has been getting money he don't want to lose all of this.
Maybe the ability to atleast set it to auto pull a certain amount of time after.
To make auto pull we need to create a subscription, but there is no a definite amount which can be used for subscription. The main idea of invoicing system is to take a percent from total amount received by a seller during a period. If you have a definite price for a seller to allow him to sell products on your site then you just need to use Membership levels. Create a paid level for sellers which allows to sell and they would need to subscribe it. So, you'll get auto payments from sellers.
From what I see on posts, we get an email, we message the customer, and no where does it say how to send money and take credits away from the seller after. Obviously I could send the money direct through my business Paypal, but how would I remove the credits from the credits holder after?
Yes, in the current version a seller should request withdraw by submitting the following form (Dashboard -> Credits -> My History page, http://your_domain.com/page/credits-history-common).
Site owner should process it in any way which will be convenient for both of them. After that he should 'confirm the withdraw' on the site (Dashboard -> Credits -> All History page, http://your_domain.com/page/credits-history-administration) and it will deduct the requested amount of creadits from seller's balance.