I don't know whether it's appropriate or not to resurrect this thread, but I am having a similar problem, only I have been following STEP rigorously and did my best to set everything up properly. (BethINI, cleaning masters, etc.)
When I enable plugins in MO2, the plugin list at %LOCALAPPDATA%\Skyrim Special Edition is accurate. I am only enabling USSEP and ASLAL. It shows both of those mods listed exactly as is referenced in this thread.
But when I start the game, the console command "coc ARTHLALFarmhouse" does not teleport me. New game leads to cart sequence. When I open Wyre Bash to review my plugin list, the plugins are visible but not enabled. I can manually enable the plugins through Wyre Bash, and then they work.
I've had exactly one time when enabling a plugin through MO2 was enough to get it working in the game. And I have no idea what changed between that time and the next time. I'm pretty certain I didn't change anything.
I had previously assumed this was a bug that had something to do with me switching from Vortex to MO2, but I'm not sure anymore. I'm using the GOG edition, if that matters.