Hi, @Ganesh Welcome to the Microsoft Q&A platform, and thanks for using Azure Services.
If I understand correctly you want to know why the difference in the default value in the MySQL docs and in azure docs.
Wait_timout was set to 120 in a single server but in flexible sever it is 28800. The reason for the smaller value is because of the single server architecture where all the connections were proxied through the gateway server. Having a higher value can keep the stale connection live and can impact other customers as all servers in a region connect to the same gateway. The flexible server does not have this issue as the connection directly lands on the server.
Hope this information helps.
Regards
Geetha
Please don't forget to click on or upvote
button whenever the information provided helps you. Original posters help the community find answers faster by identifying the correct answer.