The one problem which could be an issue is not being able to open an individual team's questionnaire until the Vision Assessment has been completed. My son had to complete the tasks in order (Profile, General Questionnaire, Medical Authorization, Medical Questionnaire, Vision Assessment Form, etc.) BEFORE being able to access other individual team questionnaires. But perhaps your son's situation could be different depending on the timing and delivery of the various questionnaires.
My son did not get specific addition medical documentation uploaded by the deadline (because I was too lazy to look for it) which seems to be OK, as long as the Medical Questionnaire itself has been completed. I figure if a team really needs physical therapy documents from when my son had Little League elbow they will request it again if it gets serious. And by serious I mean the 2020 MLB draft, not Little League elbow!
My main point above is be careful about deadlines, as in don't wait until the last minute! As someone else has already pointed out, I have no personal knowledge of what happens if a deadline passes and something is not turned in. I did not want my son to find out the hard way just in case the questionnaires are no longer accessible once a deadline has passed. Either way, I doubt it looks good to a team if you don't appear to have enough interest to be bothered with their deadline.