When you raise the front ride height, the a-arm angles at static ride height change. This affects the camber of the wheel as the wheel moves through the travel. Caster change and bump steer can also be affected. Roll center height and the way the cornering forces are transmitted to the frame will definitely change as well.
The "mechanical advantage" of the lower suspension arm in relation to the shock assy. changes. This affects the spring and damping rates at the wheel... but probably not much.
Without careful measuring and a lot of calculations and testing, it's really impossible to say if the geometry changes caused by a lift would be significant or detrimental. Some a-arm suspensions are extremely sensitive and others aren't. But with any lift on the Raptor, you are definitely risking affecting the handling... especially if the roll center height moves much... and no matter what you are raising the center of gravity of the truck.
The above is true with either spacers or preload changes. Now let's talk about the two simplest ways to raise the front end.
Spacer Method
The biggest concern I see is the full droop angles of the drive axle and the steering linkage. CV joints can bind up and you need to be sure that the tie rod end at the wheel and in the rack and pinion don't run out of travel at full droop. (don't forget to turn the wheels from lock to lock when checking the steering linkage...) The ball joints need to be checked too. It sounds like the fine folks at Truxxx have already made these checks.
One advantage to the spacer method is that at full compression you have more ground clearance!
I'm not sure I'd worry too much about the a-arm hitting the spring lightly. But if you decide to put limiting straps on to stop this contact, you will likely be reducing the overall travel of the stock suspension.
Preload Method
First an explanation of what's actually happening when you add preload to the spring. Some people will say by increasing preload the springs gets "stiffer" and ride quality is reduced. This would defy the laws of physics and is not true at all!
To keep the explanation simple, let's say the Raptor has a spring rate of 1000lbs/in. That means for every inch you compress the spring, it will exert 1000 pounds of force.
The front end of the Raptor weighs a fixed amount. Let's say with the lower spring perch in the stock position the spring is compressed 3 inches. (In other words, the spring is exerting 3000 pounds of force to hold the truck up).
Now we move the lower spring perch up one inch. What happens? Remember that the front end of the truck still weighs the same amount so the spring still compresses exactly the same 3 inches so the springs are exerting exactly the same 3000 pounds of force! But now the shock is extended one inch more which is why the front end is higher.
This puts the piston in the shock in a different position which will affect the "internal bypass" tuning.
With the shock extended one inch more than stock, you've lost one inch of droop travel (at the shock) but you've gained one inch of compression travel (at the shock).
So let's say the stock setup has 5 inches of available (shock) compression travel and 3 inches of droop travel when sitting at ride height. With the lower spring perch moved up one inch, we now have 6 inches of shock compression travel available at ride height and only 2 inches of droop available.
(Please remember that the numbers I'm using are fictional for the purposes of illustration. The actual Raptor numbers are certainly different but the principle is what is important.)
Stock at ride height plus one inch of shock compression the spring force would be 4000 pounds. With one inch of preload and the shock compressed one additional inch past ride height you have exactly the same 4000 pounds of spring force.
When the stock setup is compressed the full 5 inches past ride height to bottoming, you have a total of 8000 pounds of spring force. Compressing the preloaded shock 5 inches from ride height results in the same 8000 pounds of force.
But remember that the preloaded shock can compress six inches... one more inch. So when it's bottomed out you have 9000 lbs of spring force. (just remember what you gained in compression travel, you lost in droop travel.)
Notice that this "extra force" in our example is not there during normal driving but only at the extreme limits of shock travel. The only way to get a significantly stiffer ride around town is to change the springs.
With the preload method, you don't have to worry about the CV joint or steering linkage exceeding their limits. The only "mechanical" thing to worry about with added preload is the springs coil binding at full compression... not likely.
With either method the CV's will be running at a slightly steeper angle pretty much all the time. Will that affect their life? Probably not much if at all. (I would be very concerned about the spacer kit causing damage to a CV, ball joint, or tie rod end at full droop though.)
Either method will also affect the alignment. Jack up the front end with a floor jack and you can see the camber change on the front tires. One thing I would recommend on a vehicle as new as the Raptor is measuring the stock alignment before doing anything... then trying to get back to those specs after the lift. On some vehicles (like the FJ Cruiser), there is not enough adjustment to get the alignment into stock specs with a 2" lift...