For me, meditation started a fundamental shift in how I think about free will, and oddly nobody I've mentioned it to in real life has felt this. I used to feel very in-control of my own mind, but after intentionally sitting and monitoring for thoughts, labeling those thoughts, etc, I became sensitive to how thoughts can really come out of nowhere. You can't predict what you will think next. That strikes a little deep…
I suppose the most profound aspect is realizing that you aren't who or what you thought you were. Your free will is a facade, and it can feel unsettling.
I try to see the silver linings, like you mentioned. The first time I heard someone nail this on the head after quite a long time of sensing it, but not understanding it, was Sam Harris. I know many others have talked about this phenomenon and perhaps they've done it better, but he helped me understand it and feel better about it quite a lot. It was very unexpected, too – until that point, I'd never really listened to him.
He advocates a lot for forgiving others on account of this lack of free will, which I really like. It's maybe the brightest silver lining. I find it easier than ever in my life to let things be when it comes to external matters. I'm a lot more compassionate towards people I may have only been bothered by in the past. It's easy to get into a headspace in which I see myself in people, and recognize how I never intend to be wrong, or bad, or whatever – and that's likely no different for them.
I sometimes miss living in the facade. At the risk of sounding dramatic, I don't know who or what I am anymore. It was nice not having to consider it before. Sometimes I can't help thinking about the cellular activity and electrical signals in my body, apparently generating whatever this life is, whatever I am. It can interfere with every day life even. It can be sort of disassociating almost. I think a significant challenge going into my 40s will be finding a way to not care about these things and just let them be, and to focus on making the most of things.