I strongly agree that we lean on the Kobo update to fix things.
Having said that, I would hope Calibre might adjust it's conversion algorithm specifically for Kobo is necessary since its is the conversion which is "breaking" files. Kobo appears to require "Normal" to allow manual font changes ... that would be soooo simple to encode at Calibre.
In any case ... tons of folks here seem to be intent on DIY solutions and this might be one. BTW, have you sampled the Kobo yourself? It's a VERY nice e-ink device to hold and read from with its 6" display.