Hi, Yuyang,
Firstly, I do not think there is any documentation to remind user of the FLASHTIM&Boost registers.
Regarding your question whether it is safe to use the default FLASHTIM(3) and PBOOST(3) when the LPC4078 runs in 96MHz, I can not say it is safe or not.
I suggest you do a full temperature range test, if the chip runs okay in full temperature range especially in high temperature, it is okay.
BR
XiangJun Rong