A product of the United academy, McTominay's departure will allow the Red Devils to further strengthen their squad before the transfer deadline with Uruguayan international Manuel Ugarte expected to join from Paris Saint-Germain.
The sale of players who came through the youth system is particularly helpful for clubs to comply with financial regulations as the full transfer fee is recorded as a profit in the books.
Profit and sustainability rules that limit Premier League clubs to losses of £105 million across a three-year assessment period have been blamed for a quiet summer transfer window.
"I would prefer not to lose him because he's Manchester United in everything," Ten Hag said at his pre-match press conference ahead of Sunday's clash with Liverpool.
"He was so important for our team, for Manchester United, but unfortunately it's the rules.
"We have to discuss the rules, when you have to sell and obviously homegrown and academy players bring more value, that's not the right thing to do.
"But I think for everyone, for all parts it's a good deal, for Scott he's happy with it, for Napoli a very good player, but also for us."
There could be more comings and goings at Old Trafford before the deadline.
Jadon Sancho has been linked with Chelsea, raising the possibility that outcast Blues winger Raheem Sterling could move to United in return.
United have already spent around £150 million during the window on Leny Yoro, Matthijs de Ligt, Noussair Mazraoui and Joshua Zirkzee.
“We have a couple of conversations going on at the moment. That’s all I can say. We’ll see what happens," said United's sporting director Dan Ashworth after attending the Europa League draw in Monaco.
"There’s still a few hours to go, who knows what will happen in the last few hours. But we’ve been really pleased with the business we have done, in and out."
Liverpool advantage
Liverpool are a more mature side than Manchester United, with the advantage of a cohesive team of established players, Ten Hag said ahead of their meeting with their bitter rivals at Old Trafford.
"Liverpool are in a different phase of the life cycle," Ten Hag said. "They are a mature team with players who have played together for a long time and are very experienced.
"We are much more mixed and we have to build a new team."
United have not beaten Liverpool in the league since a 2-1 win at Old Trafford in August 2022 though Ten Hag's men did prevail 4-3 over former Liverpool manager Jurgen Klopp's side to win the FA Cup last season.
Liverpool finished third in the league last season, five places and 22 points ahead of United, but Ten Hag said his side could take heart from their performance in the cup final.
"We can always win, last year we won (in the FA Cup) in the second part of the season," the Dutchman said.
"(Liverpool) are a team who are clear in the relationship among their players. It's what (new manager Arne Slot) has inherited. It was built over the last few years."
Slot and Ten Hag have faced each other in the past during their time working in the Dutch top flight, with little to choose between them on paper.
Both managers have two wins apiece against each other in the Eredivisie, with Sunday's match at Old Trafford their first head-to-head meeting since March 2022.
Liverpool have made a solid start to the season under Slot, who became their first manager since Graeme Souness in 1991 to win his two opening league games in charge with Sunday's 2-0 victory over Brentford.
United, on the other hand, dropped their first points of the campaign when they were beaten 2-1 at Brighton & Hove Albion last Saturday.
"One of the reasons I came here is I knew beforehand it would be the most difficult thing I could ever do in my life, to come in (to) a club with a lot of problems," added Ten Hag, who took charge of United in April 2022.
"I inherited a history of six years and no trophy. We're still in transition. We have young players, academy players, and now we have to construct a team for the future."
