Yes, you can install 2005-2010 KONI struts and shocks when you use the GT500 strut mounts. I did that modification on my 2011 Mustang V6 vert. I added the shocks, struts and GT500 mounts to the stock springs, so nothing else was required. I checked the alignment and it had not changed from stock - no reason for it to, since I did not lower the car and change the suspension geometry. There are plenty of spring sets for the 2011+ cars. If you lower the car more then about an inch..estimate...you will probably need the front end realigned and may need an adjustable panhard bar to center the rear axle. I'm sure there are many on there that have done a similar mod.
You still need to get an alignment. Changing the geometry is irrelevant compared to loosening suspension fasteners and replacing major suspension components. While the car may track straight you could be damaging your tires right now.