It absolutely is a problem intended to be addressed by the GPL. That's why it is specified in the GPL that the source code means the code in its preferred form for making changes.
It's still a form of proprietary lock-in similar to not offering data export, but it's not an unsurmountable hurdle anymore.
Why not? You can decompile a cookie to try to see what method was used to make it, but Nabisco or whoever still treats that method and the ingredient ratios as trade secrets. In fact, the whole idea of trade secrets are things that are kept secret because IP protections don't cover them.