The y-alignment of plotmath is different than ordinary text:
mtext("blah", adj=0.2, line=0, side=1)
mtext(expression(alpha), adj=0.5, line=0, side=1)
are shifted vertically relative to each other. This also means that inter-line spacing is wonky if one line contains ordinary text and another plotmath.
"Fixing" this behavior requires only minor changes to the code (see bug # 14532; Brian Ripley responded to that bug and pointed out that any change to visual placement should be carefully considered under a separate report).
This is in part by design: plotmath places enclosing boxes, ordinary text uses a baseline. You should not be mixing them.
But the match is closed in the trunk.
Ah, I see. Not the design that I would have chosen, but I can see arguments for it. Thank you for explaining.