I would say that most Protestant groupings agree that the Church is an instrument. Using an analogy, if the Church is like a hammer then the Protestant groupings "took all the good stuff" but removed the unnecessary varnish on the handle. If they have this "good stuff" then they are as much an instrument as any other grouping. Thus, these Protestant groupings are a part of "The Church" because they are composed of the head and the handle.
And it must be noted that an instrument by itself is useless. Unless the instrument is actually picked up and employed for it's intended function then it is merely like a hammer sitting on a bench not performing it's intended function.
So if these Protestant groupings have the good stuff and are used as an instrument by God how are they any different than your ambiguous "The Church"?
As I said, all the good stuff that is in the Protestant groups come from The Church. There’s a lot more of the good stuff that, thanks to God’s grace, resides IN The Church. And, there’s a lot of bad stuff in the Protestant (big umbrella term incl BAptists, Pentecostals, 7th day adventists etc) that is from non-Church sources.