HTML forms are a bad idea for proposal submission.
I've written quite a few grant submission systems (I have a grant cycle running right now, with a deadline of this Friday...yay...). It's a pretty standard deal- web based system that allows for a fair amount of meta data (PIs, co-operators, institutions, name of grant, funding request, etc.). These of course are all part of the HTML forms.
BUT- the proposals themselves- the 2-20 page document where they explain the project- is always a complete mish-mash of stuff that could never go into an HTML form. Formulas, images, etc. Tons of formatting. And typically it is a document that has been shared/edited with other researchers. I ran one system about 15 years ago that was HTML only, and the number of projects that had 8 different PIs, who all wanted edit rights at the same time was way too high. This was pre-Google Wave, and the idea of 8 people simultaneously editing the same text on the web was insane then...as it is now.
Plus, the way that researchers/PIs handle these submissions is to turn everything in at the last possible minute. Any complication on the receiving system will just cause you to get your ass chewed out in the hallway at the next big conference.
I absolutely, 100% never ever want to hear someone say, "I tried to submit my proposal, I typed everything in, then there was an error." Because really, these people will open the page, then sit on it for 3 days as they dink around. When they finally hit 'submit' they're surprised that there was an error. Yes, there are technical ways to mitigate this problem...and the very best way is to have the applicants submit documents.
But, in the case of this article...I usually provide support for these systems. I've been doing this for about 20 years, so I'm fairly good at it. And the absolute quickest way to provide support to someone having problems is to say, "Just email me the document, and I'll submit it for you." 90% of the time I get an email that says, "I figured it out...thanks for your help." 8% of the time people say, "I tried to email the document, but it failed...my file was corrupt, so I re-saved it and then submitted...thanks for your help." The last 2% send me the file, I convert it if necessary, and we move on. (that's 2% of the problems, not 2% of the submissions)
There is no reason for me to make a 100% bullet-proof, all-inclusive system that will handle every single different scenario perfectly. It would take too much time. For the very small number of people with a problem, I just do it the old fashioned way. So if somebody told me, "I'm on Linux, and I can't convert my file to PDF, and I don't want to use one of the billion on-line PDF conversion tools, why is the government supporting Adobe and Microsoft!!!, blah blah blah" I just tell them to send me the file. In about 3 minutes I'm done and they are happy. Once upon a time I even hired temps to do this work- but these cases are really about .5% of submissions, and it just isn't worth it.
The article wasn't about the practical aspects of using PDF, it was about the (crap, can't think of the word...) aspect, where someone got their panties in a bunch because the government doesn't facilitate their worst-case-scenario approach to proposal submission.
Source: Been doing this for 20 years for the gub'ment. Yes, there is a guy like me behind most of those systems. See the part of the submission site that says, "For technical assistance...". Yeah, call me or send me an email and I'll take care of it for you. That's why they pay me, and good service is how I make the system look good.
***On the other hand, when you send an email to me, my boss, the funding organization and the overarching agency describing how the system does not function properly, and you were not able to submit your proposal...yes, I will send back a very detailed screenshot laden email pointing out step by step how you failed, and probably send the logs showing that you logged on one time 3 hours before the submission deadline. Goddam I hate it when people blame their failings on the system.