I don't know if this is intentional, but I seem to be unable to select custom liveries for the Legends of Great Western Class 101 consists in scenario designer, nor have I seen any spawn as an AI service in custom liveries as of yet while running any Legends of Great Western service, only if I select the custom livery for the services provided am I able to see them.
Yep, exactly the same thing happening for me too on PS4. Spent a couple hours doing a Regional Railways livery but can't even use it in a custom scenario. And because the 101 sets in LOTGW are, for some completely weird reason, standalone sets for LOTGW only, you can't use them on other routes either. So at the moment you can only use them as part of a 6 car set where it's half BR Blue and half your custom livery.