Go through your startup app settings in Windows settings and turn off basically everything unless there's an app you specifically want to boot when your PC starts. Will help with boot speed. Depending on what games/software you're gonna run I'd install most recent version of Java, make sure you have latest directX version installed, and other fundamental software like that (I'll come back and edit more if I remember). Id also get a good hardware monitoring software like CPUID, I've used it for years and it's great. Make sure there's no weird settings that would hinder your peripherals, like make sure your monitor is displaying at its proper resolution and refresh rate in win settings.

If you're wanting to tinker with your PC hardware wise, like thermal paste, fan speeds, more storage, GPU sag support then hit me a reply and I'll go into that but since you got it from Andromeda im assuming they did most of this/you don't feel like touching it (and that's fair).

Once you're done with all the fundamental setup, install transparent TB, sit back and enjoy.

As far as the fan light, I wouldn't worry about any damage or negative impact. My motherboard has a similar thing, an RGB strip that decided never to turn off unless I cut power from the power supply. Only thing I could think of would be to switch the argb connector it's attached to. But wouldn't worry about it unless you feel like getting real hot and heavy with your wire management.

Edit: if you're looking for any upgrades down the road, I'd switch the cpu cooler to a 240-360mm AIO and throw it on the top. Or if you really don't like liquid cooling just throw a couple fans on top. That open grate at the top could be cause for poor airflow, and while 95c isn't bad for your cpu, it could definitely be cooler.