I just found the --size-only flag, which makes rclone ignore the modtime entirely, even on backends that support it. If I use it, rclone will not use the MFMT at all, which means that you don't have to make a special switch for it 
Also, for those who care about modtimes, but have problems with MFMT, like me: with the --update flag rclone will update files on destination only if the source modtime is newer, and will not try to update destination file's modtime spearately (it will update automatically when the new file version is uploaded). This is ideal for me.
EDIT: I was mistaken. The --size-only flag only affects detecting file changes. If rclone detects a file has changed, it will try to update its modtime. Without the flag it thinks all the files have changed and updates their modtimes, that's why I thought it disabled MFMT, when no file have changed in size.
But --update seems to work fine in this regard.
EDIT 2: looks like --update alone does not prevent MFMT use too. Sorry for the confusion. The --ftp-disable-mfmt flag is necessary in the end.