You open linker.lsc and insert.py in notepad, then change the 800000 offset to somewhere in your ROM with a lot of free space, and starts at a new line in a hex editor to ensure it's halfword-aligned. When you do the command prompt commands, use the modified command to disable the keystone check as provided in the thread. If you set the mega evolution condition correctly and it still doesn't work, then I don't know what's wrong and I can't help you any further.
If the 800000 offset is full of FF bytes and not used by some other hack/repoint in your ROM, then you can leave it as 800000.