In the example below, is it possible to match the alignment of “Hn” and “3”?
The outer and inner labels mismatch when the inner label contains multiple lines.
The same happens with a standard font like Academico.
I believe the only way to do this is to override the instrument name, like so, using a negative baseline shift (and in this case adding the transposition back in as text):
You’d then need to apply exactly the same instrument name to the other two horns (or in my case trumpets) or the instrument name will show up multiple times to the left of the staff.
I think the only downside is that if you’ve opted to show transpositions to the left of staves in the score, but you’ve also opted to use not show transpositions in Cue Labels (in the parts) the transposition will still show in Cue Labels as it’ll be part of the instrument name rather than an automated suffix/prefix.
This all feels pretty hacky to me - I’m using my magic powers to add the “feature request” tag to the thread 
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Wouldn’t altering the baseline of condensable instruments misalign “Fl. 2” (in my example)?
I just assume that this setting would equally affect the single-line and multi-line instrument labels.
Hmm. I guess it’s a problem if the arrangement of the condensed staves differs from system to system (e.g. flutes 1 and 3 together this system, then flutes 1 and 2 together on the next system).
Exactly. I guess the vertical offset for multi-line inner instrument labels is slightly off. If you take a closer look at your example, “French Horns in F” and “Trombone” have a different vertical position than “Trumpet in Bb” (which includes a Bravura-based glyph).
That’s solely because I’d edited the trumpet name(s) and not the others
But yes, by default they’re all off.