I found this useful for getting deeper with using bash: "Pro Bash Programming : Scripting the GNU/Linux Shell, Second Edition." It is kind of a brain dump type of book but it called out a bunch of little things I had missed in looking at other information sources.
If you are starting out, keep in mind you are coming into a live and running environment. What looks chaotic to you may just be something that grew up organically over time and has an internal logic that isn't readily apparent. If they have money to pay you, they must be doing something right. Consider seeking that expertise out, even if you feel you are not necessarily being challenged at the technology level. You can always change jobs later when you have this experience under your belt. First jobs out of college are supposed to be "stepping stone" jobs anyway. "Get what you can and move on" is an entirely legitimate way to approach this.
Think about where you want to end up eventually. If you want to move into corporate-land writing reports against business databases, go for the .Net shop. If you want to eventually do "fun" stuff in startup-land, then stay where you are. Because the reality is the complexity of what people are doing with .Net is relatively low - they use it to run businesses, so you're always writing a variant of a shopping cart or accounting program. When people want to do something interesting/new/really challenging, they tend to choose other tools than those provided by Microsoft, inclusive of .Net.
So I guess if you want immediate security, go with the .Net shop. (Though be aware that in any large or even medium-sized organization you are as likely to have to learn politics as programming.)
Otherwise, stay where you are a little longer and see if you can find some value in what you have to work with now.
Seriously? Have you not heard of side channel and timing attacks? This is called information leakage and is a big deal. Because it is not common/easy now doesn't mean it won't be in the future. The nature of information disclosure (whether data or metadata) is that people find "impractical" methods of accessing information we might prefer they not have, then make them practical. It may also be the case that the researchers cannot make it practical, but that doesn't mean there aren't actors who can and possibly have already done this.
This is a very useful article OP, thank you for posting
(I am a senior technical resource in an environment like you describe. Read this after I was pretty far along but it basically sounds like how I operated to get where I am.)
Don't waste time. Be mission/vision focused. Be polite to everyone always. Be helpful whenever possible. Be insanely organized. Do not be That Guy/Gal who is always forgetting things, late to meetings, doing the wrong thing, asking stupid questions about stuff that's already been covered in meetings, etc. Seek and respond to constructive feedback on your work. Do the sh#t work without whining. All of this will build human capital with other people in the organization, which will both practically give you more resources of help from others to draw on in your work requirements, but also increases your visibility with people who aren't on the front lines doing the work (e.g. Management). That visibility gives you the means to move in whatever direction you might desire. It also (for want of a better way to put it) usually tends to help make you layoff-proof because people know you are competent, professional, and have some flexibility to work as part of a team.
None of this means you are anyone other than who you are. Don't kiss anyone's a##, but also don't be an a##hole. At the end of the day with two people even remotely similar in "technical" capability, personal behavior will matter for increasing your effectiveness within any organization.