But things like datasets are massive and structure is important. Do they retain them digitally with the same original structure or do they transform them into some kind of massive PDF?
No. See the various state rules of civil procedure concerning the presumptive and requested form of production of electronically stored information. An example is Ariz. R. Civ. P. 26.1(c)(3).
Related, I worked at a company that had a standards body forced information sharing agreement with a competitor. One of the requirements was that documentation had to be shared.
Unfortunately, our documentation was a very well formatted with links and was searchable, making it easy to navigate. So in an act of malicious compliance, the few thousand page document was printed then scanned to low res, jpg artifact filled, crooked, but still legible, set of images that were shared as a fairly useless pdf.
There was a time that would have worked because most judges didn't even know how to turn on their computers, much less the difference in file types.
Now, do the same thing and the judge would fine the company, and its lawyers, for failing to comply with discovery. And if the judge is super pissed off, they may issue a warrant for the CEO to spend a few nights in jail thinking about his decision-making process.