"the owner would use the business card points for personal travel or to purchase personal items."

Which makes it Distributed Value to them, for tax purposes.

"There was also a lot of "employee advances" categorization due to the employee paying for things that were personal in nature but wanting the company to provide reimbursement. The employee in question was one of the co-owners."

The company's funds might be used, but that doesn't make it a Business expense; that is why you post to the Balance Sheet = give that visibility.

"It was a mess and I relieved myself of those duties because I didn't want to learn bad practices and they weren't interested in changing anything. Business as usual."

You  get a lot of support, or lack thereof, from their CPA, too. If the CPA lets "employee advances" ride year after year without every settling up, or worse, offsets it to Misc Expense, I stop working with those people.