TL;DR: Because CPUBoss doesn't compare on pure performance basis, I wouldn't bother upgrading, the X5470 is better, high prices are a result of ease of use, it won't hurt anything but if it works depends on the motherboard.
CPUBoss doesn't evaluate from a pure performance, but rather a more wholistic perspective. For example, the Core 2 Duo E8400 scores a 5.9 while the i7 5960X scores a 5.8, despite the E8400 being worse by miles in every way except price.
Anecdotally, I've found that CPU/GPUBoss provide very poor metric for comparing hardware, outside of their aggregation of benchmarks and specifications (and even then, those are often lackluster compared to the original sources, i.e. GeekBench, Passmark, and ARK.)
Which processor is better?
I'd recommend looking just at the Passmark numbers. The X5470 wins with 4662 compared to the Q8400's 3187.
Is it worth the upgrade?
I'd say no. Compared to other LGA 775/LGA 771 processors and even newer platforms, the X5470 is incredibly expensive at around $40. You'd be better off jumping ship to a slightly newer platform, or investing in solid cooling (which can transfer in the future) and overclocking heavily. I won't go too in depth, but with more info on budget and requirements (read: another question) I'd be happy to.
Price of old processors
The Q8400 isn't expensive, at around $17. The QX9650 is expensive at around $60 because it's a top tier chip, and those tend to hold their value because of their ongoing usefulness as a way to squeeze a little more performance out of old systems. Notice also the X in the name: this designates it as a Core 2 Extreme processor, which–besides just being top of the line–means with it comes with an unlocked multiplier.
I won't go into too much detail, but basically, it's easier to overclock these processors than ones with locked multipliers. Compared to processors from after the switch to QPI (anything after LGA 771/LGA 775/PGA 604), where effectively only unlocked processors (K, X) can be overclocked (base clock overclocking is difficult and largely ineffective at squeezing more performance these days), FSB overclocking was common and quite effective. This lead to less demand for chips with unlocked multipliers, and thus, even higher rarity of these chips.
Xeons processors tend to hit the used market in large quantities with low prices as server which aren't economical to run anymore because of high power consumption compared to newer processors are parted out after 5-10 years. Though the delta between old Core 2 Quads and their equivalent Xeons is falling as Core 2 Quads become increasingly obsolete even in consumer PCs and LGA 771 Xeon availability falls as the server supply dwindles, this still holds somewhat true, and very much so for newer Xeons.
LGA 771 "modding'
Because the mainstream LGA 775 and server LGA 771 platforms are so similar, buying cheap Xeons salvaged from old servers and "modding" them to work in consumer motherboards allows better (higher base clocks and better binning), cheaper chips to be run in cheaper motherboards that support overclocking and other consumer features.
This does require modifications both to the chip and the motherboard in the form of a pad-flipping sticker and removing the CPU guides respectively. Though I won't go into too much depth as this isn't the focus of the answer, you can read more about it here. Note that it is motherboard dependent: Nvidia based chipsets (650i, 680i, 780i, 790i) and some Intel chipsets (P35, P45, G31, G41) should work fine, while other Intel chipsets (X38, X48) only work with X33 series Xeons. Beyond this, some motherboards outright won't work anyways; the best you can do is Google if anyone else has had success with this (since the CPUs won't be on the QVL anyways), update your motherboard as much as possible, and give it a shot.
This articles lists the E5472, X5460, X5450, E5420 (E0), L5420, E5405 as working with the mod and your motherboard.