The damage sponge motiff only works for the Atlas with a standard engine if it is being shot through side (or rear?) torsos. The trouble with this is, now that this information is known, the strategy with the Atlas is to simply core it or shoot its head off, both can be achieved simply by aiming near its head and hoping one or the other happens first.
The reason the Fafnir and the Blood Asp are more survivable, however, is because they kill or cripple pretty much anything they are facing in 1-2 salvos. I fired the 2 HGauss from a Fafnir into the side torso of a Blood Asp at about 400-500 meters on Lunacy and the entire side torso armor vanished. The second salvo destroyed the mech. Had he turned to fire on me instead of another enemy, I'm sure I would have been missing a side torso and half my CT armor from Gauss detonation. The Atlas will suffer this problem as well AND lose its Assault slot weapon, half its missiles, and 1 of its medium laser slots. At that point it lacks the firepower to be a threat to a Fafnir or Blood Asp.
I would suggest simply ditching the idea of Standard engines at this point, honestly. The benefit for a standard engine from CBT was huge over an XL, and both had their advantages. But in MWLL, where everything has been built on the idea of XL engines for everything and the mechanics for a side torso destruction are less harsh, the weight of a standard engine, with the test case mechanics currently on the Atlas, are simply not enough to make it worth it. Right now, Firepower is King while armor is only as good as the location's size.
The proposal would be to fit the Atlas with a 300 XL engine giving it 9.5 extra tons to work with. The current variants, as they stand, could then be upgraded thusly.
PrimeERLBL - RA - 5 tons
ERLBL - LA - 5 tons
Gauss Rifle - RT - 15 tons
SRM6 - RT - 3 tons
LRM20 - LT - 10 tons
MPL - RT - 2 tons
MPL - LT - 2 tons
AECM - 1.5 tons
BAP - 1.5 tons
2 LAMS - 3 tons
3 Free Tons - 3 tons
7 HS - 7 tons
EOptics -

+0.5 tons of armor
ARAC5 - RA - 10 tons
RAC5 - LA - 10 tons
RAC5 - RT - 10 tons
MRM10 - RT - 3 tons
MRM10 - LT - 3 tons
MXPL - RT - 2 tons
MXPL - LT - 2 tons
AECM - 1.5 tons
BAP - 1.5 tons
2 LAMS - 3 tons
6 Free Tons
3 HS - 3 tons
+0.5 tons of armor
BERLBL - RA - 5 tons
ERLBL - LA - 5 tons
Heavy Gauss - RT - 18 tons
LRM15 - RT - 7 tons
LRM15 - LT - 7 tons
ERMBL - RT - 2 tons
ERMBL - LT - 2 tons
AECM - 1.5 tons
BAP - 1.5 tons
EOptics -

2 Free Tons
4 HS - 4 tons
+0.5 tons of armor
C UAC10 - RA - 12 tons

UAC10 - LA - 12 tons

UAC20 - RT - 14 tons

SRM6 - RT - 3 tons
SRM6 - LT - 3 tons
MBL - RT - 2 tons
MBL - LT - 2 tons
LAMS - 1.5 tons
6 Free Tons - 6 tons
DERPPC - RA - 7 tons
ERPPC - LA - 7 tons
ERPPC - RT - 7 tons
MRM20 - RT - 7 tons
MRM20 - LT - 7 tons
ERMBL - RT - 2 tons
ERMBL - LT - 2 tons
AECM - 1.5 tons
BAP - 1.5 tons
LAMS - 1.5 tons
2 Free Tons
10 HS - 10 tons
+0.5 tons of armor
EERLBL - RA - 5 tons
ERLBL - LA - 5 tons
Lt Gauss - RT - 12 tons
LRM15 - RT - 7 tons
LRM15 - LT - 7 tons
ERMBL - RT - 2 tons
NARC - LT- 3 tons
GECM - 1.5 tons
BHP - 1.5 tons
2 LAMS - 3 tons
C3 - 2 tons

4 Free Tons
2 DHS - 2 tons
+0.5 tons of armor
Consequently, if you want to try an Atlas with a standard engine mechanic, I heartily suggest a version of the Atlas 7D and to make it sub 92k C-bills. That would make it a good and affordable damage sponge.
Atlas 7DMBL - RA - 2 tons
MBL - LA - 2 tons
AC20 - RT - 14 tons
SRM6 - RT - 3 tons
LRM20 - LT - 10 tons
MBL - RT - 2 tons
MBL - LT - 2 tons
5 Free Tons
6 HS - 6 tons
A version with advanced technology (i.e. a variant designed from the ground up to be the best sponge possible with a standard engine) could look like this.
Atlas 7D UpgradeERMBL - RA - 2 tons
ERMBL - LA - 2 tons
UAC20 - RT - 14 tons
MRM20 - RT - 7 tons
MRM20 - LT - 7 tons
ERMBL - RT - 2 tons
ERMBL - LT - 2 tons
4 Free Tons
2 LAMS - 3 tons
3 DHS - 3 tons
(Edit: Changed the Prime to be closer to canon 3050 version)