Just wanted to chime in to say that lsssk11331's method on page 2 about editing bonding points works. Using Geofront 1.0.2 patch and the table from EDIT 3 in the OP.
Just use the table from the OP, double click the address of the Mira pointer, change the type to 'Byte' and the offset to +1BF5 (Elie) / 1BF6 (Tio) / 1BF7 (Randy). That will give you the address for the bonding points.
This should let you freely pick whatever bonding options you wanna see throughout the story and also let you spam your combination crafts without worry that you won't get the final bonding scene that you want.
I tested changing the bonding points around at the place where the final bonding scene takes place and it seems that you can basically change it even right up to that point. I changed the BP totals and walked in and out of the area and the person standing at where the scene takes place also changed according. Using this, I managed to get all 3 bonding scenes in 1 playthrough + all the upgraded Combination S-Crafts without having to reload a save or do a NG+.
I don't know how the save file will interact if you load it into Ao, but I don't think it matters very much at all, since in the worse case scenario, you can easily find NG+ Zero save files floating around the internet anyway.