Hi Etienne - dual trees do work for community sources. As an example:
Tree 1: nextstrain.org/community/babarlelephant/cov/sarbecovirus-partial-rdrp
Tree 2: nextstrain.org/community/babarlelephant/cov/sarbecovirus-spike
Both trees: nextstrain.org/community/babarlelephant/cov/sarbecovirus-partial-rdrp:community/babarlelephant/cov/sarbecovirus-spike
Three trees isn’t possible, and probably never will be! I know this can be done using the python library baltic.