I think the decision to maintain an eBay Store is dependent on your use of eBay and not how you want to necessarily operate off eBay with a Commerce Store.
Example: You might want to Stock certain items in your eBay store that operate in that venue for clearance, discounts, and promotions, but keep a more standard Retail inventory in the Commerce store with a link back to eBay for the clearance, discounts, promotions. That's how I've seen many web retailers operate for years with eBay. I've often started buying from a retailer on eBay and then moved to direct purchase from their website, often with combined shipping discount. I'd message them and ask for combined (if they didn't have a combined checkout system). If eBay doesn't like it, TOO BAD, SO SAD!
If folks like what you sell, they'll track you down. That's were a registered internet address helps. Just have your methods thought-out before you take the step.
Concept for vintage clothing sellers: Sell the vintage clothing on eBay and stock a Commerce Store with Retail Clothing or "Accessories". That discussion is one I am having with group I currently support.
Danno