It is worth noting that there’s nothing inherent about there having to be pronoun number agreement or even a number distinction at all. As others noted, this happened to the word “you,” which was originally only plural and still takes plural agreement; most of us now say “you were” and “you are” instead of “thou wast” and “thou art,” while “you was” and “you is” are not standard English (though there are some who speak that way). French turned a second plural pronoun, “vous,” into both plural and formal singular. Spanish “usted” is singular, but despite being a second person pronoun, takes third person endings. Languages develop through an accumulation of historical change, which is not bound to follow rigid patterns, but there is almost always a historical background to it.
And, well, in Chinese (this goes back before the Chinese languages split), the first person singular came from a word that was originally always plural. This eventually led to a long period in which the same pronoun was used for both the singular and plural, which was also true in the second and third persons. Lots of languages don’t make number distinctions in pronouns. They still manage to communicate; context is a wonderful thing.
And when people say singular they has been used for centuries, this really is true. It didn’t fall out of use and come back; it has been in continual use through Shakespeare and Austen to now. The only thing that happened was certain prescriptivist grammarians made a claim in their grammars that singular they was wrong because they personally deemed it illogical. But this was not something that came from the English language! This was imposed, not at all based on usage.
But even if it were a completely new and invented phenomenon, which it is not, that wouldn’t matter. Language exists to communicate, to inquire, to express oneself, to be beautiful, and to cooperate with one another. It is only good insofar as it is helpful, useful, and benefits people. If people will be happier, feel better, and be more respected and validated when we use language in a certain way, that in itself is reason enough to do so. Artificially imposed constraints, no matter how self-consistent, are not more important than treating people kindly.
I understand that you’re struggling with this, but I hope this will help illustrate the background and context of singular they.