Your post is ridiculous northpit. What you're qualified to do has nothing to do with unions. Every train dispatcher is also a qualified conductor. Should their roster be dovetailed with the conductors roster? Both Smart and BLE have scope rules in their respective contracts that require "members" of that union to be used to perform certain duties, such as fair collection or train handling. Fare collection, flagging for contractors, certain yard and road jobs have to be filled by "members" of the Smart local 645/1831. Copying paperwork, arranging to enter the main, etc., are not exclusively conductors work as per the Smart or BLE contracts. If the railroad ever signed an agreement like that in the future, it would be the stupidest thing the LIRR would ever do and also restrict an engineers qualifications. Unless the BLE agreed and they wouldn't, it won't happen.
Train handling is the scope of an engineers work and by contract, you have to be a "member" of the BLE div. 269. If there wasn't a scope rule like that in the BLE contract, then yes, the railroad could qualify any craft to operate trains and use them. An engineer certified as a conductor was agreed to by the LIRR and BLE to continue to allow the engineer the ability to operate trains without conductors.
The new raise is a change in fair collection, which is exclusive work of Smart local 645 members. All members of the union are entitled, not just a conductor. You don't have to be a conductor to collect fares. If for example, the raise was for writing a train order, then the engineers are entitled to that raise as well, because they too are qualified to perform that work. But its not for train orders, its for fares.