Hey man! Thanks for your help! Here is exactly what I do:
1. Open application
2. Tools > Data > Encounter Database
3. Click on the dropdown for Species
4. Find Palkia
5. Change OT Version to Pearl
6. Search
7. Right click the Palkia and "View".
8. Only error for legality check is, "Invalid: Pokemon HOME Transfer Tracker is missing.
9. I enter a random number for HOME Tracker on the OT/Misc menu.
10. Now I click the red ! and it changes to a green check.
11. Then I change the OT from "PKHeX" to "Alex"
12. Then I change the HT from "PKHeX" to "Alex"
13. The legal check reads, "Invalid: Handling Trainer does not match the expected trainer name.
So, does the HT name have to be PKHeX? Does this show up in game? And just to be clear, I didn't change anything from the Main, Met, Stats, Moves, Cosmetic tabs and left them alone as generated by the Encounter Database. (See images below)
Side question if you don't mind: From my research, it looks like we cannot use the Auto Legality Mod with the latest version of PKHeX because the ALM has not been updated. Is this correct?