Well, I doubt you'd want to pre-charge the BCR every time you run the locomotive, the charge leaks off in a few hours. 
If you're really worried about the charging current being the issue, rigging up an inrush current limiting circuit would be the ticket. I'm going to do something similar with my MTH 44-ton locomotive. I want to add a supercap, but since it's the small PS/3 board, I'm a bit concerned that going from .5F to 2F might be too much for the charging circuit. That being the case, I'm going to add an inrush circuit to limit the charging current at startup, but it will allow full current in the reverse direction so the supercap can supply the sound when the power is removed.
