I recommend waiting with the rebase until #1789 is merged because it requires moving the tests to a new file.

I tried to play a bit with this, but encountered something that seems a bit non-intuitive to me.

This passes as Collection is excluded from the equivalence

var subject = new { Member = "1", Collection = new[] { new { First = "A", Second = "B" } } };
var expected = new { Member = "1", Collection = new[] { new { First = "C", Second = "D" } } };

subject.Should().BeEquivalentTo(expected, opt => opt
    .Excluding(e => e.Collection));

Adding .ThenExcluding(e => e.Second) makes it fail as now only Collection.Second is excluded.

var subject = new { Member = "1", Collection = new[] { new { First = "A", Second = "B" } } };
var expected = new { Member = "1", Collection = new[] { new { First = "C", Second = "D" } } };

subject.Should().BeEquivalentTo(expected, opt => opt
    .Excluding(e => e.Collection).ThenExcluding(e => e.Second));

So the equivalency engine in fact includes Collection except its property Second.

I don't think the analogy of Include and ThenInclude from EF is completely translatable and invertible to Exclude and ThenExclude.
With ThenInclude you include something extra in addition to what's being included by Include.
If you have excluded something with Exclude, there's nothing left for ThenExclude to exclude.

I think e.g. combining Including with ThenExcluding comes closer to what's happening.

subject.Should().BeEquivalentTo(expected, opt => opt
    .Including(e => e.Collection).ThenExcluding(e => e.Second));