Yes, 41 characters would be sufficient.

I would have omitted these four (the asterix being there only to have a consecutive subset):

    36 Space
    37 $
    38 %
    39 *

Especially % can be confusing, as %20AA seems like a valid base45 both before and after urldecode. The $ is a lesser footgun.

I'd be keen to learn why they decided to use full 45 characters available in alphanumeric QR.

Because you encode using 45 different characters

The GP is saying 3 base41 characters can encode 2 bytes. Using base45 doesn't shorten the encoded message size unless they increase the encoding unit to more than 2 bytes.