I just tested it with a Virtual dimmer and it does the same thing, those drivers are super basic. Basically just takes whatever commands you send and sets the device that way.
This is 100% something that Apple HK app is doing.
I am thinking Homebridge may be filtering this out, I dont think my lights do this and I have everything through HB.
I could probably have the driver block it, your example the commands are only 13ms apart. I would feel OK specifically blocking a setLevel 100 if it is sent within 100ms of an on command.