I'd like to shoot some coyotes and such when I have the opportunity to do so, and have a little 3-9x40 compact scope for my 20" RRA flattop.

I sighted it in at 100 like I do my hunting rifles, but I thought that zeroing at 200 yards would actually be better. As a matter of fact, I was thinking of going with a 50 yard zero, since that's the recommended method for the IBSZ for the carry handle. The particular bullet I'm planning to use (45gr JHP Winchester) shows a 200 zero with 100 being about 1.2" high, so a 50 yard crossover (or at least pretty darn close to it) sounds about right.

I don't plan on taking any shots which are terribly long. The rifle doesn't have a varmint barrel, I'm not the best shot, and if I miss it won't be the end of the world...

Anyone with strong feelings of one over the other ?

I zero my .308 and .223 rifles (with one exception) at 200yds for the reasons you mention.  At 100, you're only a couple inches high.  Since I rarely get a shot over 200yds in my area, this works out well for me.  BTW, those 45gr Winchesters are great on coyotes.  Hits them just like lightning.  My RRA M4gery really likes those little bullets, too.

The exception mentioned above is for one of my Rem700VS (.308) that I have zeroed at 600yds.  About 4 times a year, I visit the in-laws in W. Texas and go jackrabbit/prairie dog sniping with 125gr handloads.  6,500 acres and nothing between you and the horizon in every direction...