Ok Gnomes being slightly larger than Halflings works just fine for me. I think the more important thing is that the different kinds of shorties be easy to tell apart at a glance.
Having the Halflings follow Human/Half-Elf proportions just at 1:2 scale is the easiest way to do it I think. Because the visual read there would very different than the stout Dwarven type build.
Halflings would look like runt Humans at 1:2, and Gnomes would look like runt Dwarves at say 1:1.5 or whatever, just shrinking those model types. So the Gnomes would have bigger bobble heads and look a bit more squat following the Dwarven vibe, but standing about the same height as the Halflings. Halflings would have the smaller heads though and be the tiniest at a glance. That would be ideal I think. Just make Halflings shrunk down half elves, with a phenoptype option to be heavier set if the player wants. Give em an option to have foot-beards just for flair lol. Then they could keep their existing model work while also including Gnomes in the process. A double win!
ps. Here another one for a quick read...
Just pretend the gal on the left shows like the female Dwarf/Gnome proportions relative to Shadowheart and a Halfling on the same rock. Gnomes and Halflings would end up about the same height, but the Halflings would be clearly tinier at a glance. Then just give em all some different cloaks. Coupled with the freedom to choose a characters build/phenotype independently and I think we'd have all 3 varieties of shorty still looking pretty recognizable and simple to distinguish from one another.