Information technology requirements and issues for academic research
A lot of the things you bring up are serious issues even for the industry, and I don't see why it would be any different for academia. You should have a dedicated IT team just as if you were a generic industry organization, even if the information is open source and non-proprietary.


  Installing third-party and open-source software without waiting for administrator intervention


This is fine on a personal machine, but on a network machine, you could potentially take down everything.


  Storing and backing up unusually large amounts of data


Typically, you'd need to have backup servers, as all the research stored on-site is a great backup until, say, the sprinklers go off and wipe your data. I'd wager an acceptable plan for academia would be the same as industry. Every week or so, send a tape off to an off-site safe area to store and recovery in case of a serious IT disaster. Losing a week of work is usually more salvageable than losing everything, as happened above with those hospitals and ransomware.


  Transferring large amounts of data between institutions, through firewalls


Depending on the data, you will likely need to encrypt and password protect stuff. Especially PCI medical data. Sometimes, out of simplicity and for records-keeping, you could send a physical media like a DVD or flash drive (also encrypted) instead.


  Access to a variety of communication and conferencing tools that might not match the organization's "standard" conferencing solution


IT typically provides this as a service, i.e. e-courses. Not sure what you're expecting out of this, but "buyer beware" is typically sufficient for those that don't follow your recommendations or provided wares.


  Remote login access to work computers


We have two-factor authentication for remote log-in. If information is sensitive, that's typically how we'd store things.