Yeah there are two convenience stores that I know of within about an hour of me that are a bit defensive of their toilets.
One is near a popular fishing spot, and probably got tired of people coming in smelling like dead fish, using the toilet, and not buying anything. They have a big sign saying the toilets are for customers only, and a map with directions to nearby public toilets. They don't actually lock the doors, though.
The other one I'm not really sure what their reasoning is, but the owner installed a button behind the counter to remotely unlock the bathroom door, and you have to ask the guy behind the counter to use the toilet. There are a ton of 1-star reviews on Google mentioning the toilet situation.
But other than those two I don't think I've ever had an issue using a toilet at a convenience store.
Also on a side note - it's pretty hilarious reading reviews of convenience stores in Japan. Lots of 1 star reviews because someone was cut in line, the worker didn't say thank you on the way out, the manner in which the worker placed items in the bag, an item was not microwaved enough, etc.