With Lapua brass, I found accuracy improved when I stopped flash hole reaming, cutting, or messing with it. The hole is .059" for a reason....
Well, Lapua brass is expensive for a reason. Actually, compared to most other brass, it's quite expensive. However, it's also the most long lasting and is literally ready to load.
Not so with something like Lake City. Take a look inside the cases sometime. Lapua has a nice flash hole which appears as if it's drilled. Lake City looks like it was shot with a small caliber rifle and there are often large ugly burrs on the inside.
I haven't tested flash hole de-burring alone as it relates to precision groups but I have spent some time fine tuning my cheap brass to include careful trimming, chamfering, flash hole de burring, primer pocket uniforming, annealing, and sizing in attempt to make a silk purse out of a sows ear. There is definitely an improvement in performance with carefully prepared brass but I can't say what percentage (if any) is attributable to improving the flash hole.
I would say it makes sense that a flash hole without a bit ugly burr would better and since it's only an additional two or three seconds time on my case prep machine, I do it with cheap brass. I already have the case in-hand from chamfering so sticking it on the deburring tool for a second or so is no big deal and I only have to do it once.
But, since Lapua is so well made, it's not necessary to dress it up to this extent. And, as you pointed out, messing around with a perfect flash hole is not likely to improve things.
Bottom line: If your flash hole has a big burr, get rid of it. If not, leave it alone. Now you have my two cents.