Were those 5k included miles written in the contract as only to states adjoining WA, or nationwide? I suspect you could pay a lot more than expected.
Imagine if you were several thousand miles away from the nearest Sixt. And worse, if that Sixt was an independent franchise with no corporate-owned cars available for an exchange.
I can't help but wonder where the original GLC was registered, and where the replacement X3 is originally from. Sixt just doesn't have the flexibility for one-ways and exchanges like competitors with a nationwide corporate presence.
Also, how did you "waste" the time in San Antonio? Surely you visited the tourist attractions? Unless you already made nonrefundable plans to be somewhere else.