Mail Smart Folders across accounts / between Macs

OS X Mail Smart Folders are very useful, but I have one problem:
My "Unread" folder between accounts and Macs has two criteria: Unread, plus on one account, not in a certain Inbox. Now, the mail account that I use for that 2nd criteria is only set up for use on one account. I have 2 accounts on my Mac Pro and 1 account on my MBP. When I check my Mail Unread folder on the other account and other Mac, the Unread folder syncs across iCloud, but since that email account I use for the 2nd criteria is not set up (active) on the other account / Mac, the Unread folder essentially breaks. If I edit it, then it breaks on the other user account where that 2nd criteria is effective.
Does that make sense? Anyone else having iCloud Mail Smart Folder sync issues across accounts / Macs?
Running OS X Yosemite all up to date on everything.

iCloud does not support or sync Smart Mailboxes or local folders. You can create mailboxes at the iCloud.com site that will be IMAP and show in the Mail sidebar under the iCloud folder. Those will show up on all devices.
Other than that, iCloud will only sync Mail's main mailboxes (default mailboxes).
In Addition to better explain:
Local folders under On My Mac are folders only located on the computer. They are not part of any IMAP or Exchange account.
Smart Mailboxes are for the most part just search engines. Messages are not stored in those, but they merely point to messages which actually reside in the original mailbox where they are stored.

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