If you need to configure SCP-specific options, it means that you want to use SCP, so you should switch to SCP explicitly.
In other words, if you do not care about protocol, why would you configure protocol specific options?
If SCP specific option are enabled when primary selection is SFTP, it makes user think that SCP options apply to SFTP as well.
And that actually looks like your problem. You seem to try to fix problem with SFTP protocol with options that does not affect it at all.
So what problem do you actually have?
In other words, if you do not care about protocol, why would you configure protocol specific options?
If SCP specific option are enabled when primary selection is SFTP, it makes user think that SCP options apply to SFTP as well.
And that actually looks like your problem. You seem to try to fix problem with SFTP protocol with options that does not affect it at all.
So what problem do you actually have?