Does MITObim bias gene order?

[liamfriar]

Has anyone tested if MITObim has a bias against genomic rearrangements relative to the reference given? I want to use MITObim to try to circularize a bacterial genome that SPAdes assembles into ~200 contigs. I have a good circularized reference genome from a related strain that I can give MITObim along with the reads. I am worried that MITObim will tend to put genes in the same order for this new assembly as they are on the reference genome, even if there have been rearrangements. This genome contains a very large amount of transposases and other repeat elements. Does anyone know if MITObim deals well with these? Thank you!