In terms of the Bold app - that makes sense since their code also needs to fire on the form submission. Leaving the ajax enabled will interrupt of conflict with that process.
The Product Customizer app (from memory) has some support for file uploads. For that to work you must submit the form via html - without Ajax. If all the app does is add extra line items to the form I would have thought this one could have worked ok. If you've got feedback from the app maker that it won't you'll have to trust that's really the case. They will know better than anyone.
The bigger question is what are you using those apps for? I checked out your products and couldn't see a great deal of things that you'd need custom options for. Depending on what you need you may be able to build a feature into the theme to skip using an app entirely.