...on the other hand would it be worth creating an MP option to differentiate between patch enabled games and non-patch enabled...
If the C&P would be included, of course there would be an option to enable it or disable, so admins of OTTD servers could decide. Also there can be limit to pasting intensity. These options will exists even without trunk inclusion.
If the paste action becomes a DoCommand then it shouldn't be to trival to hack a client around the protection mechanism if the server is configured to disallow paste...
As Zuu said, someone can write the patch to hack this option as long as C&P is based on DoCommand chain. But this is already possible, you can use C&P in servers where this patch is unwelcome (there is not many of them, I always ask on the server forum about C&P before using it). So trunk inclusion has no negative impact on this issue. Even otherwise - it eliminates this problem!!!
If the C&P would be included, there would be server side support and C&P would no longer use DoCommand chain. Old mechanism would be discontinued, thus not available as a patch.
I don't think that any programmer with enough skill to continue patch in old form (DoCommand chain) has interest in cheating in MP games. Besides, how many patches do you know that are made for cheating? They surely won't appear in this forum or flyspray.
Maybe I'll implement server side support when the patch is completed, but these are far away plans.
don't worry, be happy and checkout my patches