I'm staying at 2 resorts this trip, and I did my own ADRs online. I don't think the question of where I was staying even came up. My last two visits were also split stays with Disney ADRs. I can't think of why your resort plans would confuse your dining reservations.
As PP stated, there can be questions about technicalities of the dining plan program, for example, how the dining plan operates on check-out day of first resort and check-in at second resort, or, having to buy basic park tickets for both reservations if you are using the dining plan at both resorts, etc. IMO, your TA needn't have made a comment unless a specific question arose. There's plenty of visitors who do split stays, and dine at Disney, and have no issues. I don't share your TA's concern.