A total re-glue is a massive job... mainly getting all those overlapping sections off without damage and then cleaning it up to a proper standard. And you'll need warmth plus low humidity to use the new glue.
Can you continue pulling this apart further than where it stops at the moment. Have you also looked very carefully at all the other parts of the transom and the floor-to-tube glued seams.
I use a soft plastic scraper to see if I can prise the seams apart.
Yes it is possible to make a strong repair to the problems you've found if that really is the extent of the failure.
Perhaps a professional who was charging you for the work might not be happy just doing sections but my belief is it's fine for a DIY job... you will have to keep an eye on all the seams from now on though.
Have you seen my thread from this summer where I carried out even more complex localised repairs to the old Aerotec I owned...
Aerotec patching/glue advice.
Despite some choppy water testing at speed since then every repair has stayed strong.