The size differences you mentioned should make no difference in mounting those 2.5" HDDs. There is a maximum thickness defined in the 2.5" drive form factor, and any size difference will only be smaller than that. The manual did not have any warnings about the height/thickness of the HDDs.
The manual was unclear about using two SATA drives plus the mSATA drive. The HM77 chipset supports up to six ports, so that is not the limitation, if one exists.