What about stats of flamer ammo?
And if i remember correctly Penetrate worked different on tla (something like -20 dr )
TLA flamer ammo is stronger than in reloaded: (its -15 AC and -10 DR, keep in mind that AC has a different function in TLA)
^TLA
^Reloaded
About penetrate perk:
^Reloaded
^TLA
15% DR reduction is likely better than the DT/3 reduction in reloaded.
So you are right about the penetrate perk, the flamer mk3 should probably do more damage than the improved flamer (120-140) for example.
Disclaimer: I take all this info from the Reloaded Wiki. And as we know, the wiki has plenty of mistakes. So dont blame me.