As you say, Iran has all kinds of large commercial aircraft hanging around, with access to more. Why would they need a 777 for their hypothetical plot?
IFF, radar cross section of jet and its engines, to place some doubt in the minds of the pilots ordered to shoot it down if it is painted like a Delta or AA or United or BA etc... Just to be sneaky? Who said they were smart? Besides, who wants to buy a used Malaysian 777 with all matching S/N parts for that aircraft?
Since everyone is open for speculation....what if it was not the plane they wanted......but some engineers who know a crap load about designer chips... implantation into terrorist etc...after all, knowledge is power, these men have or had a lot of it apparently ....I dunno just sayin... However it is probably waiting to be found on the bottom of the ocean somewhere....anywhere....batteries and all :/