Rolf, I would expect those lines not to change at all.
Eily, thanks -msc pointed me in the right direction.

After some more experimenting, I've found that this code:

    $d->{status} = 'queued'; # something
    $d->{description} = 'The action'; # other thing
    $d->{id} = '12345'; # Identifies action
[download]

gets changed to this:

    $d->{status}      = 'queued';     # something
    $d->{description} = 'The action'; # other thing
    $d->{id}          = '12345';      # Identifies action
[download]

...which is definitely better in that case.

But even if only the last line had a comment and I use -msc=1:

    $d->{status} = 'queued';
    $d->{description} = 'The action';
    $d->{id} = '12345'; # Identifies action
[download]

...it still pushes the comment way out to the right to align with some non-existent other comments. That's not necessary.

    $d->{status}      = 'queued';
    $d->{description} = 'The action';
    $d->{id}          = '12345';     # Identifies action
[download]

Setting -ols/-nolc don't seem to have any effect on this.

And now I've found what I was looking for:

-ssc -sscp=#
[download]

This sets "static side comments", and sets the identifier for those to the usual # character

docs: http://perltidy.sourceforge.net/perltidy.html#static_side_comments

This lines up the equals but leaves the comments alone. The only time the equals doesn't get lined up is if that would make the line longer than the -l setting, which is fair enough.