How to change SQL sever configuration manager settings using TSQL? SQL server configuration manager is used to configure certain settings like connection protocols, service start up,  etc... 
Is it possible to make these changes that is done in SQL server configuration manager by using TSQL statements, or in the SSMS?
Most settings that can't be done via sp_configure are registry based

So, you can use xp_instance_regread etc to change them. You'll have to find a list of registry keys yourself sorry but most are under HKLM\Software\Microsoft\Microsoft SQL Server

One examples , protocols is under

...
...(instancename)\MSSQLServer\SuperSocketNetLib\Tcp
...(instancename)\MSSQLServer\SuperSocketNetLib\Sm
...


and each of these has an Enabled value 

One important note: you can stop SQL Server from xp_cmdshell or using SHUTDOWN but not start it of course...