Allright. I see that you have cut in half the size of LVCA update_info by removing 1 duplicate changelog.
You are maybe right that LVCA isn’t responsible.
It did just turn on a red light that the function taking an unreasonable amount of time set_site_transient() update a record in the DB table wp_options with a 36KB long field where a single entry was 13K (LVCA one) whereas most of the others are all smaller than 500 bytes.
I did retest this afternoon with the changelog duplicate instance removal (now your entry takes ~7KB) and the function is even few seconds longer than yesterday…