Although I agree that ‘it seems wierd’, my friend did hear it from R’ Chaim himself [he said its based on the Vilna Gaon].
I think it does not “cause tzarros” but rather can be “meoroer the midas hadin” and [sadly] nobodys perfect.
zichronolam.com mentions the concept, as do other websites that deal with sta”m, and they are also makpid on it – in any case i don’t think it was “made up”.
If I was getting new mezuzos, I would for sure get ones that have this.