It's as flexible as windows if you are a programmer and happen to specialize in *nix programming, specifically for the pi as it has limited resources. If not then you are s.o.l. and since 99% of the users aren't, yeah.... not nearly as flexible.
I understand what you're getting at here, but allow me to be a bit pedantic and clarify that you don't have to be a "programmer" to customise a Linux OS with different tools and software.
I'm not a programmer, but I do happen to be a Linux sysadmin by trade. So yeah, piece of cake for me to do what I like with this device. If I need more power than a Raspberry Pi can offer, I still use Linux by choice, because of my skillset and the flexibility that Linux offers over Windows (again, assuming you know how). But certainly no programming knowledge needed.
On that topic, familiarity with Linux is not hard to obtain. It's ludicrously well documented, and I've brought people up to scratch with decent Linux skills and no prior experience in as little as two weeks (a bit part of my job is training folks from scratch, and I offer this to people in my local gaming community for free). The problem most folks have is that they try to treat Linux like Windows, get frustrated and fail, But being "different" isn't the same as being "difficult". Folks forget they've got 20+ years of Windows experience, and confuse that with it being "intuitive".
Anyways, I get what you mean above. Yes, Raspberry Pis are great if you're a non-Linux-user and want to use the images provided, but can be daunting if you don't have the skills and know-how to modify it beyond their defaults. Same goes for any software, even Windows. Working in corporate IT, I've seen my fair share of folks who can barely find the MS Word icon without a call to IT Support. Not everyone finds Windows "easy" either.
Replying to the OP: Most emulation software under Windows doesn't require "installation" per se. You can generally just get your setup running nicely in a dedicated subfolder, zip that up, and transfer it to another system with ease. Things like MAME and RetroArch store all their configs in handy text files, so use that as a basis to do your config once, and then transfer it system to system later on, with minor tweaks from a clean Windows install other than telling it where to find the frontend to autostart on boot.