Is there an approved way of fixing a cracked Fiberglass Tub/Shower?
I'm not familiar with the second approach but, as you say, it would address the root issue of the tray flexing when in use and should prevent the problem recurring. It also does seem to be rather radical.

The main drawback I can see is that you are causing more "damage" to the tray and therefore increasing the risk of the repair failing.

I'd ask the company if you can contact (or be contacted by) someone else who's had this done so you can ask them what they thought of the procedure. Ideally you'd be able to see the end result and check out for yourself before proceeding. If the firm is reputable they should have no problem with this. In fact refusing this would be a sign that the firm wasn't as reliable as they made out.