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I'm surprised you assert this. Until I encountered the Shimano quicklink mentioned, I've always joined Shimano chains with the Shimano chain-tool, whose design makes it impossible to drive the pin too far. (I imagine this accounts for a good number of chain failures.)
Shimano chains joined in this 'traditional' fashion ran and changed smoothly and have not yet delivered me to a fiery death. To be fair, neither has the chain joined with the quicklink but it was a devil of a job to fit — I had to take the bike outdoors to ride, and give the pedals a proper kick to get it pull up tight.
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The margin for error gets smaller every time the plates get thinner. The joining links have essentially eliminated user error from the equation, which is a good thing. I can't speak for Shimano as I haven't used one of their chains in decades, but certainly KMC and Wippermann joining links are easily worth their price for making the job simpler and quicker, even for a user with the skills and tools to create a riveted joint as good as a factory one.
FTFY.
I would not, under any circumstances, join modern narrow dérailleur chain the "traditional" way, it's asking for fiery death.