You didn’t provide any information on your nationality, so I can only assume that you are both aliens, and of non-Chinese ancestry.
According to the relevant legal regulations, a person who obtains any type of resident visa (which would include JFRV) should apply for an Alien Resident Certificate from the local Foreign Affairs Police Station within 15 days. At the same time that the ARC is obtained, a Re-Entry permit (sticker) will be put in your passport.
Although you may have your daughter’s passport physically in your hands, nevertheless there is no record of her having entered the country and passed through customs. Hence, it will be easy for the authorities to verify that she is not here if they do a computer check.
Based on this analysis, it makes little sense to apply for a JFRV, with the required next step of getting an ARC and a re-entry permit. What if in the next few months the Police notified you that they could find no record of your daughter’s entry into the Taiwan area, and wanted both of you to appear at the Police Station for questioning?? That wouldn’t look nice.
Normal procedure would be to physically bring your daughter in on a tourist visa, and then apply for her resident visa (based on her relationship with her resident visa holding parents) after she was here.