Should I worry that it's not going to be installed using an USB stick?
Not sure what you mean by that but installing from optical media works fine too.
I like SFF computers but we rarely get asked to build them.
My current gaming machine is also the polar opposite, it's in a Fractal R6 Define (non windowed) which is a full tower with mount points for anything from ITX to ETX. Not sure why you'd put an ITX in a case that size but they included mount points for it on the tray.
I own a business that normally builds to order high end bespoke workstations or gaming PCs that require a full tower case to fit everything in and enough cooling to keep them stable. Servers and anything else 'standard' are ordered off the shelf from Dell, Lenovo (include Fujitsu in that as they are part of Lenovo these days), or HP. We don't have the capacity to build and support everything, plus it is cheaper for clients for us to do it that way when we are supplying an entire new network or large scale equipment upgrade.
Years ago I won a Shuttle ST20G5 barebones from a computer magazine and a copy of Office 2003 Pro. That was a nice quiet little machine that fit on the monitor shelf I had once I'd bought the necessary components to make it a working system. The ICE cooling was reported by some reviewers to be very noisy, they had it configured wrong because it was whisper quiet.