I see no logic in it!
I don't think it is supposed to be logical, it is supposed to serve a function in the rules, and we are seeing an odd interaction.
The limit on Bonus Action spells is to prevent powerful unforeseen combinations, they have learned from the past that letting full spell casters get two full effect spells off on their turn can be game breaking.
The ability to use your Reaction to cast spells like counterspell are in place to for the spell to work as it is intended and for what I think cool exchanges between spell casters having a duel of sorts.
I think they should change the wording on Bonus Action spellcasting to "The only spell you can cast with your Spellcasting action on the same turn you cast a bonus action casting time spell is a cantrip." That way it wouldn't stop the I used my reaction to cast a spell now I can't cast a bonus action spell issue.