I get the distinct impression that HD3 went from concept to production in a very short space of time. Too short, perhaps.
Of course Keysight's engineers could lay out a board with a CPU on it for themselves, but that's not something which adds a great deal of value to the product. It's not something which is "special", it just either works or it doesn't. So if someone else already has a board with the right combination of CPU and memory on it, it's likely quicker to just use that. Also, having the CPU and its memory on a different PCB means the two boards can use different geometry and stack-up, so there's a cost saving and possible yield improvement too.
What other clues?
The industrial design, for one thing. HD3 isn't pretty. It doesn't have a clear brand identity; remove the label and it could have been made by anyone. Nobody spent any time on it, or thought it was worth putting in that extra effort. Nobody loved it.
Round the back there's a Displayport connector, not HDMI. Either would work, but I know which cables I have lying around and they wouldn't fit the HD3. I wouldn't have called DP the obvious choice, but could it have been: "which one can we confirm right now, so we can get on with the rest of the schematic without further delay?", rather than having to wait for an HDMI licence?
And, of course, not forgetting the firmware. Missing features at release isn't what we've come to expect; in fact, the extent to which the firmware is fit for purpose has always been a defining characteristic of 'grown-up' scopes (as compared to their much, much cheaper Chinese competition).
Has Keysight been caught napping? Did they perhaps think they were ahead of the curve with a high resolution ADC on the way, only to realise too late that even a $400 scope comes with one these days?