Hello Robert,
Turns out the reason Aeroflow chose to use the LS2 stat in the LS3 housing is because they wanted to maintain the swivel feature of the housing. The LS2 thermostat is smaller in OD allowing enough space between the bolts to but the thermostat in and still swivel. They are aware that the Thermostat will not reach the bypass but also know that it will not effect the cooling capability of the system. At most the engine may warm up at a different rate.
On another note. Our Autoplumb brand of LS 1&2 housing utilizes a standard SBC/ BBC Thermostat. We also have experience no issues with the thousands of units we have sold. You are correct in that there is a slight change in functionality but the issue is which one do you want Swivel or functionality that doesn’t seem to matter. I hope this clears up the concern you had. If you should change your mind and choose the swivel function I believe you will experience no issues with the Aeroflow housing.
Best Regards,
Joe
@Autoplumb