My 140mm rear fan and both 200mm top fans (yes I have the extra one installed) all easily reach the fan headers on my MOBO. I could plug my 200mm side GPU fan into one of the mobo fan headers but then I would see the cable through the side window. Only that side fan and the front fan are connected directly to the PSU but my PSU has molex -to- 3pin adapters.
The cable for the side fan really is short but my guess is that is done on purpose so you can easily connect or disconnect it when ever you remove the side panel. I have the cable tucked down under the bottom of the HDD cage so it's out of the way and not visible through the window at all. My MOBO has a total of 6 fan headers, 4 of which are along the top so I guess that's why I had no issues with all my exhaust fans and CPU cooler easily reaching a fan header.
I would like to know how the side fan on your Lvl10GT is "better". It's the same size, same speed, same air flow. The only difference, and it's in the HAF X's favor, is the HAF X side fan has an air duct that helps channel that air directly onto the GPUs. An open fan like in the Lvl10GT does blow air on the cards but with out that duct the air has the chance to dissipate before reaching the cards.
If for what ever reason you don't like that air duct it is removable. Just to compare fan options between the two cases
Lvl10GT: Front Intake 200 x 20mm; Rear Exhaust 140 x 25mm; Top Exhaust 200 x 30mm (single only); Side Intake 200 x 30mm; Optional Bottom Intake 120 x 25mm
HAF X: Front Intake 230 x 30mm; Rear Exhaust 140 x 25mm; Top Exhaust 200 x 30mm (with option for a second identical fan); Side Intake 200 x 30mm; Optional VGA Fan Duct 120 x 25/38mm; Optional VGA Bracket 80 x 15mm.
So in comparison the Lvl10GT has fewer and in some cases smaller fan options when compared to the HAF X. The only thing I will give a nod to is the optional bottom in-take fan. But the HAF X has a larger front intake fan and an option for a second top exhaust fan and that space can be used for a radiator allowing you have have a radiator but still keep the stock exhaust fan in place. The HAF X also has the option to have a total of 3 different fans blowing air directly onto your GPUs. Those extra GPU fans do not make a huge difference but if you are running an SLI set up every little bit can help.