Blacklisting Mods
By Group
Synthesis Groups can blacklist mods. To do so, click on the Group of interest, and a UI should show that lets you pick the mods to not include during patching of that group.
By Patcher
Patcher Settings
Individual patcher developers can decide to offer patcher settings that expose a mod blacklist as they see fit.
If a patcher does not offer the setting, it is something they can decide to add. Perhaps add a request on the patcher's Github page.
Synthesis Provided Per-Patcher Blacklist
Synthesis itself does not provide functionality to blacklist a mod for a specific patcher. There's an issue for it in the works.
In the meantime, if a patcher does not offer a mod blacklist within its own settings, your best option is to put the patcher by itself in a Group and use the blacklist it offers, as described above.