Will aftermarket short arms make a huge difference? No.
Will they make the ride and handling better? In my experience, yes.
However, one of the biggest gains over stock arms is you don't have to worry so much about bending the crappy stamped arms which can handle no rock rash or big hits at all
I am talking about the control arms themselves, not the bushings. Nothing is perfectly rigid so you can consider the control arm itself as a spring. The stock control arm is stamped from 14 gauge sheet metal and provides a certain level of "spring" on its own. Aftermarket control arms are much stiffer, hence less spring and harsher ride.
All clear now?
True, but flex joints give you the "spring" required what the stock flexy CAs would do under a load that would make the arms twist. Driving on the roads, CAs mostly transmit only longitudinal forces anyway, so what affects ride quality and NVH the most are the CA angles and bushings used - not the amount of flex the arms provide.
As for the bushings, flex joints do have poly bushings but if the aftermarket arms have stock- style clevite rubber bushings on the other end NVH does not really increase much at all IMO. Most of the time, we're running MTs or ATs anyway which will create quite a bit of NVH anyway
The bigger tires with more sidewall on the other hand do absorb some of the energy from sharp bumps that stock tires wouldn't, so they do some good as well
As you mentioned, a short arm lift is a short arm lift. With 3.5" of true lift, no short arm lift will ride as good as the ZJ rode when it was stock, no matter what kind of CAs one is running. Aftermarket arms adjusted to some WB stretch (~1.5 on both ends) will ride better than stock arms, but one shouldn't expect any miracles
1998 Grand Cherokee 5.9 LX daily driver, 1.75" BB, 32" KM2s, HPD30 Eaton e-locker/D44a stock LSD, 4.56 gears, custom- fabbed tube bumpers and tube fenders,...
1990 XJ Limited (4-door), 4.0 I6, AW4, NP242, ***rolled and totalled @ 165k miles***
1990 XJ (4-door), 4.0 I6, AW4, NP242, PBR 42" tires, Unimog 404 portal axles, 110" WB, full cage + uniframe completely rebuilt, front 3-link + panhard / double triangulated 4-link rear,... ***SOLD***