We had the same question playing two players with one token left in the reserve. We played lose the last token and take a token from the discard . It seemed punishment enough not having any reserve token. We decided to do the same with no reseve tokens if that occurred.
Regarding where to place the regained token we interpreted "your board" as the nautilion and the rules clarfies on page 21 that this includes the mages cabin if using that expansion.
I can't think of any reason to put the reclaimed token on the phantom board. This wouldnt count as your board afaik.
The general theme of the blue cards seems to be more favorable to the player than the red Darkhouse cards. We took that into consideration when deciding wheter to activate the effect with less than two tokens in the reserve.