While the protag is forming the harem, and the girls don’t know about each other, he simply isn’t justified. He is a two-timing asshole, even if his end goal may not be malevolent. But he may be forgiven.
When there is absolute honesty from the onset, there is no real cheating, and thus no need to “justify” cheating.
Favouritism, however, would be a different (and complicated) matter.
As Avaron1974 points out, threesome relationships are much more viable than larger harems, unless they simply are a case of “bunch-of-roommates-with-benefits”. Human nature and all that.
When the harem is just united by subservient, starry-eyed admiration for the “alpha”, it can get boring very fast. And as a means of conflict resolution, a rushed, shoddily written, out of the blue discovery of bisexuality just doesn’t cut it. (This from a bisexual.)
I’m not against harem routes in general, but they must be well written, and, for me, the characters involved must be intelligent and with big personalities. Most harem routes fail these tests.
Sisterly Lust is an example of a game on here where this is done acceptably well (to date).