I found a workaround to play Downfall Mode using the Mystery Dungeon characters, but workaround does require another mod and the use of dev console.

1. Download the custom act mod known as Acts of Hallownest. (and the Act Like It Mod as well)

2. Make sure dev console is enabled in "BaseMod"

3. Start up a "The Pokemon" run in Downfall Mode.

4. When prompted to "Choose Your Destiny" choose "Greenpath". For some reason, Acts of Hallownest overrides Downfall's custom Neow event with the default one, which Mystery Dungeon itself can override to give the Pokemon selection options.

5. Choose your Explorer and Partner as usual.

6. Once you are given your starting relic and before you choose a Neow's Blessing option, open up dev console.

7. Type the command ">act Exordium". (If you want to play a different custom Act 1, replace Exordium with the name of the custom act 1 you want to start with.)

8. You should now be playing your chosen Explorer Team in Downfall Mode. Due note you will need to save and return to the run when you enter the first encounter to reset the music, otherwise, you will have to listen to Greenpath's and Exordium's music playing at the same time.