United have already had one 28million pound joint bid turned down but seem certain to go back with a higher offer before the transfer window closes on September 2.
Moyes' successor, Roberto Martinez, has already said he would not welcome the continued interest.
However, Moyes feels if the same situation had occurred last summer, when he was still at Goodison Park and Sir Alex Ferguson was still in the Old Trafford hot-seat, he would not have stood in the players' way.
"I definitely (have sympathy for Martinez)," Moyes told reporters.
"But I also know if I had been Everton manager and Sir Alex (Ferguson) had come asking for Baines and Fellaini I'd have found it very difficult to keep them.
"I always thought the right thing to do was the right thing for players."
Although United's present stance continues to treat Baines and Fellaini as a pair, there is an acceptance they made need to split the approach if Everton's resolve to keep Baines in particular does not weaken.
Former Toffees goalkeeper Neville Southall has been unimpressed by United's approach, accusing Moyes of lacking respect for his old club by trying to complete a cut-price deal.
Moyes is adamant that is not the case.