Were they? Bobs updated even before I did, so I guess I never noticed. I was a little late to the 0.17 party though. Angels definitely took a while longer though.
If you already have a save game that you want to continue, I wouldn't recommend it. If you're willing to start a new game, then yes, there should be no issues.
This issue only exists because FXP Transport (not Storage, for some reason?) modifies the vanilla storage tank to have a t2 upgrade, but mini machines does not create a corresponding t2 upgrade (due to not detecting bobsmods), and doesn't overwrite this data. Being a 2x2 entity, it cannot be upgraded into a 3x3 entity, so Factorio throws an error.
If you do want to continue your current save, I am still in the process of working on a full compatibility version.