If you are comfortable with editing the script, you could just comment out the call to the NTP_Ready() function in the SCMerlin script.
Most of Jack's scripts want the NTP clock set first before the script runs. Even NTPMerlin, which on the surface is kind of counterintuitive (I mean, that is the whole purpose behind running chrony - to set the clock). The real issue is a lot of Asus stuff depends on, or waits for, the NTP_Ready NVRAM variable to be set to 1. I was able to get NTPMerlin to work ok by bypassing the NTP_Ready() function, but other built-in router functions gave me nothing but trouble until the NVRAM variable was set to 1. Manually setting the NVRAM variable works for a while, but I think the watchdog function sets it back to 0 if the Routers NTP client is not updated as the variable would get set back to 0 after a while.
For something like SCMerlin though, you should be able to bypass the NTP_Ready function.