Yes. As a stock replacement, a low-ohm coil would certainly cause those problems. The Microsquirt allows dwell (and accordingly amperage) to be fine-tuned and limited. Default dwell is 3 ms. From
this page:
To control your coil for maximum performance and reliability, you must set the maximum dwell parameter for your MicroSquirt? controller. A couple of points are that few automotive coils are designed for more than about 6-6.5 Amps, and reduced coil resistance has been used to shorten dwell times as engine rpm limits have risen over the years (shorter dwells means higher rpms before the dwell is cut back), so as a result most coils are between 2.0 and 4.0 milliseconds, with a general trend towards shorter times for more recent designs and longer times for older designs (wasted spark and coil on plug can be different, of course, as they fire less often and thus don't get cut back until a much higher rpm).
That page has a calculator that shows the amp draw based upon input data. I do not have inductance data for the Subaru coil, so I will have to try it and see. If I recall correctly when I laid out the wiring and amp draws, I budgeted 5 amps for the coils. Using 3 ms of dwell with the Super Coil will keep me under that (4.63A). If it turns out the draw is too high to charge the battery with both, then I'll have to try the Emgo coils.
EDIT
This page has some detailed and relevant info. The author tested a number of motorcycle coils using resistance in ohms (O) and inductance in milliHenries (MH) and listed specs for each. Using their numbers with the calculator, I can determine amps (A) drawn at dwell settings:
Kawasaki points coil:
O: 4~5.1
MH: 13~16
Using the calculator and average values, this returns 2.99 MS of dwell @ 1.59 amps.
Kawasaki electronic ignition coil (should be similar to GS OEM & the Emgo replacements):
O: 2.4~3.2
MH: 7~8
Using average values, this returns 3.22 MS of dwell @ 3 amps. To get 3 MS, it would draw about 2.88 A.
Accel (motorcycle) Super Coil:
O: 3.1~3.8
MH: 15~18
Using average values, this returns 9.21 MS @ 3 A. At 3 MS, it draws only 1.62 A.
As a side note, the Accel Neon Super Coil is rated at .54 O and 7 MH, so it would draw 4.63 A for 3 MS of dwell.
Dyna gray coil:
O: 2.2~2.9
MH: 8~9
Using average values, this returns 3.33 MS @ 3 A.
Neon aftermarket coil:
O: .6~.7
MH: 4.98~5.03
Using .65 ohms and 5 MH, this returns 1.36 MS @ 3 A.
To get 3 MS, the draw is right at 6 A. At 2 MS, the draw is about 4.25 A.
Dyna mini-coil:
O: .5~.7
MH: 3.3
Using an average ohm value, this returns 3 MS @ 8.4 A.
Looking at the end results, I'd say that the Dyna min-coil and the Neon aftermarket are excluded. The Accel motorcycle Super Coil gives the most dwell for 3A of current. The reviews I've read about it for performance seem to be favorable but like a member commented here mounting is the issue. From a power usage standpoint, the Kawasaki points coil uses the least- but does it provide optimum performance? Wasn't there a reason why the manufacturers (Suzuki & Kawasaki) lowered the primary resistance when going to an electronic ignition? I'm sure there is no free lunch here.