I would guess that since the soil in the trays would be going with the lupins when transplanted, starting indoors would be fine.
Apparently there are multiple forms the inoculant can come in, which would determine how it should be applied; hopefully it comes with instructions. Expect you're right that inoculating after any other prep is done would be best, so as to not wash it right back off; if your inoculant can be applied as a liquid that might kill 2 birds with 1 stone.
As far as inoculation in the wild, this abstract suggests that, at least for those sorts, the rhizobium spread on their own through the soil... very slowly, and mostly downhill.
http://www.sciencedirect.com/science/article/pii/003807179390200U
This would imply to me that transplanting Lupins which had previously been inoculated would be a good way to help spread the rhizobium around, and thus make life easier for any volunteer lupin.
'Theoretically this level of creeping Orwellian dynamics should ramp up our awareness, but what happens instead is that each alert becomes less and less effective because we're incredibly stupid.' - Jerry Holkins