I agree with you about generation of reports and other things for widely considered submittal. I was extremely productive in grad school and was spending my time on the subject at hand, not on technicalities and drudgery, precisely because for every homework problem or lab report I could do "make submit" and it'd end up where it was supposed to. Even graduate engineering students routinely seem to waste insane amounts of time on clicking their way through the most rudimentary of changes that, once you have scripted the process, become so routine you don't even think about them.
Ansys, for example, is a usability 7th circle of hell until you realize it demonstrably wasn't designed to be used normally in point-and-click mode (maybe it was, but the designers were on crack the whole time). You can point-and-click a bit to get a feel for things, but if you want reproducible analyses, you must script them from the start all the way to generation and saving of the plots. I would not trust any FEA done in Ansys unless accompanied by a script that starts with a system in default state and ends up with output files you're after (raw output, tabular data, plots).
Same really goes for, say, generating plots or generally data-dependent drawings in Office. Once you're down to populating the entire document from a template in VBA, it becomes even less hassle to do it on a Unix system using Latex and makefiles. Never mind the basics like version control. Text-based scripts and formats really mesh well with diff tools used with version control. VBA embedded into Office documents is not handled by normal differs; you pretty much have to whip your own to dissect the OLE compound file and feed the extracted text via diff. The work needed to maintain such a tool (I've had it for a while) is simply not worth it when in the text-based Unix approach it simply works quite effortlessly. Good luck to anyone wishing to develop a blame tool for Excel, for example - good luck dealing with figuring out who did what in to an Excel spreadsheet otherwise.