That is a good question BM. I usually include the mast in my models, but I also realize a mast is just another consideration that can ill-affect how an antenna design works, and it can show up in the antenna results.
If you look back at other models done by many of the antenna gurus on the Internet, you will probably find, if you can tell, that they hardly ever include the mast in their models. Most of the time you won't even know if there is a mast or know how high the model is set. All of that can be important.
When I first did my Merlin, sometime back, I did not include the mast. The other day when Homer made this thread I opened the model and just went from there. I posted it just to go along with my showing him the feed point similarity in an image I got from Cajun. I never thought we would be comparing the Merlin to the A/P either.
The problem arises now that the A/P requires a mast to make a good match and work as intended. The Merlin models I have are absent the mast. Not a really good approach for a fair comparison.
I still don't have the true Merlin dimensions, and the top part is just my best guess-ta-mation, so this all may be a vain effort.
I think I have completed the comparison work and got the two models close to the same settings for accuracy and the segment count, but I still want to study the results a bit more.
Homer, you're going to be surprised at the results so far. I know I am. Be aware too, that these Merlin models still have their ground plane radials set at about 40* degrees, and I suspect that when I bring them down some more closer to 20*< degrees, the gain will improve. This of course assumes that the match does not go to heck in a hand basket.
I the Merlin even compares close to my Starduster, then this recap report I did in the spring of 2011, probably suggest why.
View attachment Signal Recap 2011.pdf