"a vpn does alter the route the data is sent from your isp to the server"
show me where that is wrong at all because that's exactly what a tunneling service is meant to do.
That's correct. You also stated this:

however, a vpn does alter the route the data is sent from your isp to the server so it does DIRECTLY alter data.
Which is not correct at all. Changing the route does not amount to changing the data.