If choices and thoughts just happen, then what kind of agency does the self have?
It, too is a creation of the unconscious mind. It tends to stay conscious for a period of a few minutes, then fade for a few seconds while we scan the environment, then it recreates.
You can track this in an MRI scanner with the "default network", or by meditation, or by psychedelic drugs (careful with that last one).
Then realize that the "death/rebirth" of the self occurs multiple times per day, not once per life, and re-think how you understand religion.
And each re-creation of self can be a new entity, a chance to drop an old thought/habit and pick up a new.
You should have some attachment to earlier "yous", love is real and powerful and you should love yourself, but those prior selfs are not the totality of you and you can also love without attachment, mark some of that prior self as past and gone never to return.
My wife threw out some cut tulips this morning. They still had their petals, but they were cut a week ago and she thought they were fading. She really loves tulips.
So to consciousness they suddenly appear, but it was still my brain that formed them, so me.
Interesting philosophical position! I've rarely seen that position be held in earnest, because the obvious consequence is that you should be held fully responsible for anything possibly criminal you do while sleepwalking, as it was still on your brain's orders, regardless of your state of consciousness.
There have been experiments on split brain patients (where there Corpus Callosum has been severed, so their two hemispheres no longer communicate), that seem to imply that the self is more of a way of monitoring and understanding what's going on and tying it all together.
For example, asking the subject, whispered in one ear, so only one hemisphere receives the request - "can you get me a can of Coke from the vending machine please, I'm really thirsty". Then when the subject returns, asking the other ear (and hence the other hemisphere) "why did you get that can?" - to which the subject replied "I thought I would need a drink on my way home" - in effect filling in an explanation for the "black box" behaviour their body was expressing.
I'd say that agency is your executive function's ability to take control of the actions resulting from that process. Someone who binges after starving lacks agency, because their executive function has lost control, while someone who holds themselves under a cold shower is exercising agency by staying there in violation of thermoregulation, pain, cold shock, or whatever else.
I don't think agency can be defined outside the context of the process that is you. Determinism and randomness are inherent in that process, and someone operating predictably still has agency so long as they're exercising control.
I started meditation about 5 months ago, via the Waking Up app by Sam Harris (after reading the book of the same name).
He is extremely keen on this notion that "self is an illusion" and keeps trying to help us app-users see that.
As a n00b, I can't answer your question with any authority. To me, in my personal practice, the evaluator of these thoughts still feels like "me".
When I intentionally set out to think about a problem, iterate on possible solutions, pick an approach — also me.
What I really feel subjectively, after daily meditation practice for a few months, is that the human mind is made up of a whole bunch of sub-entities that can produce "thoughts". Words, images, a visceral sense of forboding, or joy, or anticipation — all "thoughts".
To paraphrase the famous trilogy, there are hoodoos in the matrix.
For me, this was weird and kind of unnerving to realize. At the same time, it's only based on my subjective experience — and I have already proven that my subjective experience is an unreliable guide, because a lot of what I previously felt like were the authentic thoughts of myself, which I, myself, me, was thinking, were in fact just some quasi-random crap thrown up by the various hoodoos in there, which had just happened to bubble up to my consciousness at that time.
Anyway I am pretty sure that many people have spent their entire lives trying to answer your question, lol.
What I can say is only that, the trying of it is pretty interesting and enlightening (at least in the prosaic everyday sense of the word).
It can also be a bit disorienting and even alarming. So the OP is surely right that some people are probably better off not meditating, although I feel confident that most people should probably try it.