If you would define a letter for a piece in the promoted series, WinBoard would consider it just another piece, with no relation to the corresponding basic piece. Thus the corresponding basic piece would not be considered promotable, and the piece would remain itself on capture (provided there is space for it in the holdings).
When played as variant alien nothing of that matters, as the engine sends board updates anyway, and thus decides how things promote and how things would go into the holdings. The only thing is that you would get nonstandard SAN and FEN. But the letter form would not have worked at all in the standard edition, when played as variant shogi. Fortunately upto 4.7.2 all standard editions ignored the setup command.
With
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#PNBRQFEACWMOHIJGDVLSUKpnbrqfeacwmohijgdvlsuk
P.BR.S...G++..++..L..Kp.br.s...g++..++..l..k
One thing that further complicates matters is that in Shogi the Queen is displayed as Lance symbol, so what looks like a Lance is internally really a Queen. This is a legacy from before the invention of the pieceToCharTable and flexible mapping into the holdings (compacting out all the unused pieces), when it was mandatory that the pieces participating in Shogi were consecutive encodings. That there also is a Lance in the promoted series was to be able to use that pictogram also in non-Shogi variants (e.g. for the Spartan Hoplit Pawn). Shogi had to mess with the way pieces are displayed anyway, as I want the promoted partners of P, N, S and Q (=L) to all look like the Wazir W used to represent Gold, as these all move as Gold.