Trust... but verify.
In my case, with the FPGA outputs, I already knew the frequency and the DS1054Z counter was exactly correct. But, you're right, it's good to verify.
I had two goals for the scope: Check SPI with 4 channels, triggering on CS' and looking at acceleration, velocity and displacement simultaneously on my analog computer. The Digilent Analog Discovery does a terrific job for both of these uses.
I haven't modeled the damped harmonic system but I did just model a circle and displayed it in the X-Y mode. First, it works! And Measure-All gets what is an entirely reasonable answer for Vp-p and so on. There are a couple of things I need to play with: First, I don't seem to be able to increase the persistence in X-Y mode and to accommodate this, I need to speed up time on the computer. My base time is 1 second and 10x is 0.1 second. Next evolution, I will incorporate 100x. Good stuff to know! Second, the X-Y display is under the YT display and it's in a little box. I need to study up on that. But, heck, X-Y is simply a diversion. Time to read the book, I suppose! But first the adventures...
There is indeed some variation in triggering, even on edge, as a function of the trigger level. Nothing I haven't been able to work around (change the level to get what I want) but, yes, it is apparent. I particularly noticed it when decoding RS232. Not just triggering RS232, actually decoding it. Unless the phase of the moon is just right, there is every possibility that the decode is wrong. Twist the trigger level knob and things clear right up. I'm not sure I understand all I know about this issue.
Coming from an analog scope, the part I find the most confusing is the fact that the trigger point is in the middle of the screen by default. Yes, I know I can move it but, still, I'm used to traces starting over on the left. It'll take a while.
As it stands today, the scope is doing everything I had hoped for. I really have no issues. Even if I had issues, I wouldn't be willing to spend a great deal more money to buy something else. I read a thread where somebody wants to skip over the Rigol and move to an R&S scope. It has three times the bandwidth (great!), half the channels (sigh...) and five times the cost! I'll pass! This is just a hobby...
There are probably only two people on the planet interested in analog computing but I find it gives me much more insight into the differential equations I was barely able to handle back in college. Things would have been a lot easier if we had had analog computers in the lab.