Elastomeric vs. 100% Acrylic for Hardieboard
" He didn't want battens so he used urethane in 1/4" joints. He then ran out of money."
I'm pretty sure he ran out of money first, so he didn't install battens. 1/4" gaps will eventually be the source of water intrusion.
"Is there any reason I couldn't use a masonry primer?"
A masonry conditioner, (Sherwin Williams Loxon), is a good choice for the 1st coat, especially if it's still factory primed.
"... and then topcoat with Elastomeric Paint?"
Recipe for disaster. Big 1/4" gaps , water gets behind painted surface, elastomeric keeps it there...cue the bubbles.
"Elastomeric Paint is a thicker coating and would hide the shadow lines"
Yes it is and no it wouldn't.
"The house has a good vapor barrier and if water got behind the panel it could weep out from the bottom."
Not sure if you're referring to a vapor barrier or a weep screed, but it hardly matters. Applying an elastomeric would provide no advantages and several disadvantages. Much better off installing battens, using a masonry conditioner, then applying 100% acrylic topcoat.