Besides, lee makes the cheapest POS equipment in the world so i have a hard time taking their manual too seriosly.
The Speer #13 manual has the same warning, and only in the .40 S&W section. It does not specifically mention Glock (to the best of my recollection), but does state to that there are known problems with reloads in guns that don't fully support the cartridge.
That said, yeah, if you have a Glock with polyagonal rifling (or any pistol with polyagonal rifling), it's not advised that you use lead bullets. Some folks use plated bullets instead, with no ill effects, some just stick with straight jacketed bullets.
Just be careful in your process and you should be OK, even if you use the cheapest POS equipment in the world. Be safe.