The sole proper solution is to account for SQLite limitations in those migrations by altering them. However, I would not suggest to merge migrations if it is deployed to a staging/production environment. Local environment does not matter at all.
I also have to account for SQLite limitations very often, e.g. could not drop 2 columns in 1 single transaction so had to create two separate Schema::table blocks in the down method. The plus is ofcourse tests that run on multiple threads, which I will happily take.