Could you describe the part in red with more details?

The writer is being figurative when he says "the Web opens the workshop windows." He's likening the dissemination of scholarship through the Web like air flowing through a window. He's contrasting the Web with the scholarly article which he asserts was (it's interesting that he uses the past tense. What, aren't scholarly articles written any more?) an attempt to freeze and mount some part of the scholarly process for display.

It's saying there were two phases of research work before the web: the process of doing the research and writing it up, and then the second part--everything required to get it into print--the submission to a journal, the editorial process of deciding to publish it, the submission to peers for review, their comments and possible revisions based on them (maybe several rounds), the actual editiong into a printable form, the actual printing, and the distribution of the journal (each stage of which can take months, sometimes rising to years). But putting it on line reduces that whole second part, after the research process, to a single click of a button. (of course it can also mean that there's no check before everyone sees it that the data were good, the methodology was sound, and the analysis made sense. Now that all has to come after it's online, and some research can turn out to be bogus as a result). It gets there much quicker, but there are fewer checks on its validity.

Cool.

I wonder whether "that" above equals to "whether" in meaning.

Thank you InfraBlue.
IMHO, the past tense particularly denotes an era (of paper) has gone.