Joss is one of the few nicknames I think works equally well for a boy or girl.
I'm actually in a similar tho kind of reversed situation. I want to use the nn Joe but, tho I like the name Joseph, I wanted something a bit different. Hence Josiah.
I actually really like Joe, but I'm a fan of "regular guy" names on little boys. I think they're fresh among the Kadens and Aidens and Sebastians nowadays.
Jack is a bit trendy to me, but I do like it a lot. Jagger not so much, altho maybe just Jag would be cool? I quite like that, actually.
In real life, the only Joss I know is a girl whose full name is Jocelyn, so I tend to think of this as a girl's name. For Joseph, I just like Joe, which has a nice understated sound to it, but without anything "average" about it. As a little boy, I'd call him Joey.
Re: Jody, I have known a male Jody, but he got a lot of teasing for his name and as a slightly below-average-height little boy, got into a lot of fights (maybe to defend his name?)
Joseph Arthur is a great name! And I think Joss is a great nn for Joseph! I'm not familiar with Joss Whedon (though it does sound vaguely familiar), but I will admit that for the first ... year or so after I heard of Joss Stone, I thought she was a boy. I hadn't heard her music, obviously, just about her and I assumed from the name Joss that she was a boy. So obviously I find it incredibly masculine.
Also ... this may be a reach, but nicknames are all about what feels right to the parents, so ... what if you called him Jasper? All the sounds are there in Joseph Arthur, and it kind of sounds Jasper if you say it fast ... just throwing it out there since you like it so much but can't have it. Could be another option where you both get what you want. :)