I have selected 6” SCH 40 (0.28” THK) pipe of MOC SA-335 P11 in PVELITE. Why it is asking to check PWHT box when it is not mandatory per Table UCS-56-3 (b)(1)?

Anyway you need a minimum preheat of 250°F (120°C).
I mean PVElite assumed that you are following the rule which is PWHT. You prefer the exception, which is - in your case- no PWHT but preheat.

You are correct mariog. But Pvelite software have the option of selecting "Preheat" which is currently disabled for MOC SA-335 P11. In my opinion that option shall be available.

As a very personal opinion, I think you expect too much from a software. Strictly speaking, in case Intergraph wants to modify the software, UCS-56-3 (b)(1) says that you may replace PWHT based on three coincident conditions: limited thickness, limit of carbon content and preheat. I mean the alternative is that the software has to have a loop where you have to mark the conditions up as fulfilled.
In my opinion, the judgement to apply an exception is an engineering one and you have the possibility to add in your report something like "PWHT requirements replaced by Preheat, based on ....".
However, P11 as well P22 are notorious to be sensitive after welding and some codes limit the hardness. I guess PWHT is a better option than replacing it with Preheat, even your Code is more permissive.