Hi Javier,
Unfortunately this is a long-standing problem in Converter, but it has never been highly prioritized in order to be addressed and fixed. I guess the assumption was that "it doesn't hurt" to have logical partitions. It is the first time I hear this is causing actual problems - added free space at the end cannot be used unless switching to dynamic disks. We should need to revisit this bug again and prioritize it accordingly.
As a workaround I would suggest that you can resize volumes as a part of the conversion process - you can add free space to each volume in the conversion wizard and would not need additional resizing after that. I know it is not a real fix but it might be enough for your case.
Regards,
Ivan