Looking at PAC's website, it appears that the only difference between the AP4-CH41 v1 and v2 is that the v2 works with both amplified (Alpine and HK) and non-amplified (base) systems whereas the v1 was only amplified systems. Best Buy has the v1 on sale for $209 right now so I ordered it and then saw that the v1 was discontinued. That explains the discounted price but I also want to make sure that it will work for my HK system. Additionally, it appears that everyone that has posted so far about the AP4-CH41 was talking about the v1 before there was a v2 so, again, it seems that the v1 will work as expected without any issues.
By the way, if you order from Best Buy, make sure you search for AP4-CH41 and not Amp Pro or AmpPro because the first time I searched for Amp Pro and accidentally ordered the AP4-CH21 which won't work. They are both the same price so just be sure you order the right part number.