"until the deadline for the Release of Transcript Restriction."

The link is different--if you have access, the latter filing will be available through Pacer due to the expiration of the deadline mentioned in the docket entry. Previously, it was only available to the general public at the courthouse, and not through Pacer. Of course, it's never available for free through Pacer. But the transcript would just bore you to death anyway. This has nothing to do with any "long version" or "short version". By that, you are referring to the Judge's Written Order, not the transcript of the Markman Hearing.