Where can I add a cover letter or motivation section for my visa application in Thailand?

In the same section as where you upload your library card, your swim certificate and your driving license.

All not asked, but who knows it might help to explain why you think you need a visa.

IF the Thai Government was really interested if you could use a keyboard, the question was added to the application website. Please follow the instructions as mentioned on the website and stop believing all kind of advice to upload your great grand fathers pictures at a temple in Thailand to proof the need to search for your roots.

There is no section for this, just combine it with either your location, or your financial, or documents PDF upload.