When I was able to use FTM I never merged and I still had problems.
At least two current Windows genealogy programs and one Mac program can handle large databases. For me having ruled out the possibilty that they deliberately do not fix it, to upset people, there are two possible reasons.
Firstly the interaction with Ancestry militates against it working efficiently.
Secondly the cost of fixing it is so high in relation to annual budgets and profit on the product (if any) that it doesn't make sense for the small number of number of individuals involved.