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Imagine party A has 23%, party B has 28%, and party C has 49%. Party A and B join forces; they decide per consensus on how they would vote in parliament. Since they have together 51% and vote as one, they don't need to consult party C, even though it's the party with the most votes.

We have again a situation where 51% crushes the 49%.

[Someone]

That's only true if party A and party B agree on every decision, in which case you simply have two parties, "AB" and C.

Also, in some countries, there are way more than 3 factions (over a dozen in Belgium and the Netherlands), making it less likely that the same subset of parties will find itself in agreement every time.

The effect of having that many factions is that the majority part of parliament will always take the minority opinion into account because they know that, in the next vote, they may be part of that minority.

Of course, that is not a guarantee; I think it is part of a nation's culture. Other countries may value the short-term "let's win this vote" way above the longer term "we have to live in this country together".

That certainly seems the case in the USA, where "in four years time, we might end up with the shorter straw." doesn't seem to play a big role in politics (?anymore?)