Not sure why you're seeing the 41% penalty, rather than a heavily reduced penalty. Normally, ENG lower the penalty for urban or woods attacks, but have very little firepower of their own.
I use one division with ENG per Corps, and they're noticeably more effective against cities, woods, and river crossings, but substantially weaker than my other divisions in the open plains. Just as with AT, they're ONLY effective in certain circumstances, and in any other situation, nearly anything else in their place would be more effective. A 3xINF+ART or 2xINF+2xART will shred a 2xINF+ART+AT in most situations, or a 2xINF+ART+ENG in open terrain, because the unit with the specialty brigade gains practically no Soft Attack from that brigade, and the Hard Attack of an AT brigade is wasted on a completely soft unit. Even most Armor Divisions have several soft brigades, so AT isn't dramatically more effective against those divisions than ART or INF. Use ENG and AT sparingly, position them where they're needed most, and you'll probably find yourself with a far more effective fighting force than if you spam them into every unit.
INF+3xENG might be useful against the Maginot Line (90% fortification penalty), but in any other situation would be pitifully ineffective considering how much you paid for it. The 3xENG give a massive reduction in terrain penalties, but if you don't have a reasonable amount of firepower to modify, what's the point?