Return of the evil potato
Essentially yes. Msleeper changed the name from "@command" to "command" and added a logic_auto output to give you the gun. Since it's no longer called "@command" it can't be controlled by sp_transitions_list.nut.
Yeh i just deleted the @command from my "custom_ents.vmf" because i saw it had no inputs... and so far nothing has changed in looks...
However, should i be concerned that this will perhaps mess up some other game element/entity?
I just start the player in a seperate small room outside the map with a weapon stripper in it, (that should strip the potato gun,) and at the same time teleport the player from that room to the elevator with a regular portal gun in it. This should be quick enough to work fluently and shouldn't be noticible.
Why not just not use the transition_ents? You can place a player_spawn, portal gun, and trigger inside your elevator and get the same effect. Place the player spawn about 8 units above the trigger (just above the floor) and set it to activate the elevator. When you spawn, you'll fall 8 units into the trigger that gets everything moving.
Unless you plan on making a mappack with multiple maps and a custom map list, the arrival_departure_transition_ents.vmf isn't needed. And as for global_ents.vmf, you can simply copy the parts you want to use into your map.