First of all, TC does support a submenu within a single menu element, witness ace-of-penguins, OSS, and others.
What seems to be suggested is targeted merging with alpha sorting with categories defined within the menu of Applications (extensions).
This is one of those areas that you can please some of the people some of the time, but not everyone.
Those that use few extensions would have to navigate down to extra submenu while currently they do not.
If you find yourself always using the same set of applications, you can choose to disengage from the dynamic menu creation without programming changes, Do such by deleting or commenting out the <Include>/usr/local/tce.menu/menu</Include> line in your .jwmrc and instead merge in your existing /usr/local/tce.menu/menu to .jwmrc and then edit to your liking. Note by such decision, you are opting out from further dynamic menu creation. So it depends on how you use your system and how dynamic the application set will be,