Timer in CTC mode to generate 1MHz pulse

As described on the page I linked to, each timer has an A and B side, and those sides can be commanded to toggle/set/clear a fixed pin, as per this table:

Timer 0

input     T0     pin  6  (D4)
output    OC0A   pin 12  (D6)
output    OC0B   pin 11  (D5)

Timer 1

input     T1     pin 11  (D5)
output    OC1A   pin 15  (D9)
output    OC1B   pin 16  (D10)

Timer 2

output    OC2A   pin 17  (D11)
output    OC2B   pin  5  (D3)

So, OC1A can affect Arduino pin 9 (pin 15 on the actual chip).

I mean, the goal here is to enable the timer/counter interrupt mask register (TIMSK1) so as to enable timer interrupts and this is the point of that line.

Yes, but you can't process interrupts that fast, as I said. The hardware however can toggle the pin at any reasonable rate. Instead of using interrupts, let the hardware do it. In any case, interrupts can be out a bit if another interrupt happens to be active at the time (eg. Timer 0).