The first version you sell to a user at full price and offer a discount for upgrading (something like 40% off). It lets the customer pick when they feel the value prop is worth the cost and lets you offer a loyalty incentive to the user.
Right now the choice is "keep paying for it to keep working" or "fully price for every upgrade".
Since then, people have backed off.
If you're going to this much work to help users workaround Apple nonsense, you really care about helping them save money, and the support + refund costs of people accidentally buying the bundle with the old version they don't need is > just building out your own server-side system, versus a combinatorial explosion of bundles in the App Store that creates a confusing minefield for users.
Panic even had an upgrade for MAS users when they released their new version of the now defunct Coda outside the MAS (for sandboxing reasons).
It does not look like a problem for them.
Do you have an example of a company that saturated the market with free upgrades and went down because of it?