I'm using SourceTree for macos, when I add account, choose ssh key option is missing. It allows me to use only id_rsa, but I have to use separate key ~/.ssh/custom_github.
Any idea how can I proceed?

I was having the same problem on mac. There was no option within SourceTree to change keys.
However, I did use the information here to get around it.
This will generate a new key from within SourceTree for a particular account.
Not the exact fix you wanted but got me over the problem.
A dirty workaround:
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