the warning comes from the drones mod, and will trigger anytime the player changes surfaces (teleports to a different map). factorismo uses surfaces, and the surfaces mod obviously does. As far as I know it isn't harmful, but yeah the message will trigger anytime you go to or from Naavis [main map].
Would suggest a config option to author to "disable drone multi-surface incompatibility console spam" [or something to that effect] so the message won't keep bugging you.
this is of course, unless these two mods are completely incompatible.