Wow, that is so hardcore to send a firearm back to the factory via a FFL. Really ridiculous law or rule. California makes things hard for honest law abiding gun owners. It's worst there than Hawaii's gun laws.
California is not requiring a person to send a firearm back to the manufacturer (or to any other FFL) from an FFL. Apparently, one person at Glock is telling the OP to do so.
I've sent three Glocks back to Glock in Smyrna, GA.
The first one I used the dealer as they only charged my $25 for the packaging and shipping charges. The bad part was the FFL didn't get to shipping it right away and it took ~week fo it to get to Glock. As I received a new frame, it did have to come back through a dealer and I used the same dealer for the "re-dros'ing".
With the second Glock, I shipped it myself, but it cost ~$80. The good part was Glock had it the next day. Again, I needed a new frame and Glock coordinated with me as to which dealer I wanted to use. Again, I used the same dealer for the "re-dros'ing".
The third Glock I shipped back resulted in the same gun/frame being returned and it was shipped directly back to me. As there was no DRoS involved, the entire shipping, repair, and return took ~week, but did cost me ~$80 again.
The original poster's main issue will be whether or not an off-roster frame will be returned. I don't know if a Gen2 is on roster or not. That's one question.
Another question is can Glock ship a non-USA Gen3 frame/gun back to the OP? If this is the case, then there should be no problem re-dros'ing the "new" gun.
If it's a USA-made Gen3 frame, do check with the FFL, but it's my understanding USA-made frames are not on the Roster. But check with the FFL as the FFL is the one subject to any California audit.
There's a bit more, but it shouldn't have anything to do with the mere shipment BACK to Glock. It probably has more to do with what's being shipped back to the OP via an FFL as the OP already told us he's getting a new frame.
If the OP can get (via an FFL) a new Austrian-made Gen3 frame in exchange for his Gen2 frame, I see no problems. Anything other than that, check with the FFL. I'd say the person at Glock is wrong to require the FFL to ship the original Gen2 gun back. California does get complicated. Do understand that California is not making the OP ship via an FFL back to Glock.