The cable outer is probably too thick for that drain hole, and it will be out at an awkward angle so won’t look pretty.
If you’re brave, you can (carefully) drill your frame to run it. Search MTBR forums for a thread about that. Liteville has a PDF document somewhere online with instructions on how owners of some of their older frames can drill out their seat tubes to fit stealth droppers. Not saying this applies to all frames, but just throwing out some ideas :)
If you have bottle mount rivnuts in appropriate locations and don’t need bottle cages you can drill one out one and run the cable through the BB shell and up the seat tube.
Or just return it and get the regular version, but put a cable tie on the cable anchor cover so that you won’t lose it.