Ref 9 is like dac3se with a few changes, namely dsp1 but also improvements in multiple areas. If audio-gd added dsp1 along with the psu upgrade they usually do when updating their dac's from df1704/pmd100 to dsp1, it quite bridge the price gap between dac3se and ref 9 by almost half (or maybe more), and the other sound-related upgrades account for much of the rest.
But I still think the dac3se is probably a better bang for buck. There is one upgrade that may be more cosmetic than functional, which is the nicer chassis, but audio-gd does say the newer chassis has less syntony, or vibration. Also, the dac3se has not had its price increased to reflect inflation for a relatively longer amount of time than the ref 9, or to reflect the update to R core transformers (kind of hard to believe they gave the dac3se R cores without raising the price hehe, I still suspect this is a misunderstanding).
But still, if you really want dsp1, then just get the ref 9, because you won't convince audio-gd to add dsp to the dac3se when there's a dac right above it with dsp1 being the main upgrade.