Batteries

I've done a bit of research about this as well and from what I can see on the web and general advice from people wiser than I is that linking the two for charging will shorten the life of both batteries.

It is perhaps not the ideal arrangement as the two battery types have slightly differing charging requirements. However, neither the AGM nor the Flooded Deep Cycle will receive the "ideal" charge from your alternator even if used alone so it hardly matters anyway.

Some people will maintain that connecting a pair of dissimilar batteries in parallel will somehow cause some interaction that harms the batteries. It does not. If healthy, each battery will absorb an appropriate amount during charging and each will contribute an appropriate amount to the load when discharging.

The vehicle alternator, as designed, recharges the cranking battery using a simple constant-voltage method (too crude to be described as an "algorithm"). This is less than ideal for the deep cycle auxiliary batteries but that is what they get in most installations.
A better way is to leave the alternator and cranking battery arrangement as-is and install a DC-DC multi-stage charger to charge the deep-cycle battery from the alternator supply. Such a charger will provide the charging algorithm that is better for the deep-cycle batteries.

Joining two batteries in parallel when being charged by a multi-stage charger is also not ideal even if the two batteries are identical, so it is better to have a DC-DC charger for each battery (as I do) but it is now becoming a bit expensive. Also with this arrangement it is not possible the have the auxiliary batteries in parallel to feed the load. The load must be split and allocated to each battery. (as I have)

So in summary, I would say go for it. Just connect the two batteries in parallel and charge them from the alternator via a battery-isolator. You have little to lose.