Yes, I see you were trying to "disable the prescaler", but "Figure 14-1. Real-Time Counter (RTC) Block Diagram" doesn't show any bypass path.
> there is no way to use an external clock and have a low prescale value?
I think the expectation is that the "external crystal" will be in the megahertz range and not in the kilohertz range.
Maybe you can use the "Timer/PWM" module in "Output Compare" mode to generate faster interrupts. It looks like it should run directly from the external clock.
It doesn't look to be flexible enough to have one counter running from an internal (fast) clock and another one running from the external clock, so if you're already using the PWM this may not be an option.
Can you run the FLL locked to your external clock to get a crystal-accurate internal clock, and then run the RTC or PWM from that?
Tom