If you are using the Lemmy software, which is open source, that is just an interface. (plus their are other Lemmy apps and web browser uis that aren't maintained by the original Lemmy team. By not using their server that's you dedicating resources into your own type of community that is govern differently and is clearly not the same as the default Lemmy.ml instance.
Since the software is open source the main simple, straight to the point difference is who is running what servers you are federated with. Using Lemmy also doesn't automatically mean you are supporting the Lemmy devs since they are not profiting from ad revenue. They would ask for donations.
I stated that using Lemmy (the software/app) doesn't / does not automatically mean you are supporting the original Lemmy devs. What I was mainly getting at was, when I said, "Since the software is open source the main simple, straight to the point difference is who is running what servers you are federated with." but that also certainly extends to the the server you are on as well.
No one is saying stop using Lemmy over this, in my opinion, it's because not one person or company owns all of Lemmy servers and communities. So the difference really lies with the specific people running your servers and communities. Can you trust them, can your instance provider trust them. Do you trust them or your instance provider.
That is the difference.