Is there some clause in the contracts that says apps from same source will count as single app, no matter how many times they are uploaded as separate app?
It could easily fall under a fraud or abuse clause. If you decide to play games, Apple would be more than happy to pull their authorization and ban you out of spite. Now none of your apps work.
It's unlikely but they could also pull a google and ban any company who hires you in the future.
How do you provide updates after removing it from the store?
OsmAnd has more than 10 million installs, VLC more than 100 million. Can you imagine the fees? They obviously don't have hundreds of thousands of dollars on hand to pay every month to Apple.
VideoLAN (VLC developer) is a non-profit so they are exempt from the Core Technology Fee even if they distribute on an alternate app store.
"OsmAnd is developed by a Dutch private limited company, OsmAnd B.V. located in Amstelveen, the Netherlands"[1] so it looks like they would be subject to the CTF if they choose to distribute from an alternate app store or utilize a non-Apple payment processor; or they could stick to the existing business terms and continue as-is in the Apple App Store.
This actually affects small devs as well. It's not that hard to hit 1M installs for free or inexpensive apps.