No, the special mods are (or at least were) only possible to get at creation time, not by quality upgrades or re-engineering.
That's why if you want PEN, OVER, SPR, etc you craft a pile of beams or torpedoes at mark II VR until you get that mod.
For things like Omni beams that you have to craft at Mark XII we're out of luck.
(Apparently the engineering duty officer crafting missions can get you gear with special mods too, but again if they don't arrive with the mod you'll never get it.)
You also can get Pen and other mods with items created with Doff assignments, but obviously, what you get is RNG.
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Not for weapons, but one of the most useful mods for me in crafting is the [Inertia] on crafted engines.. +10 is wonderful for the Buran!, but back to weapons, just fabricate a bunch of MK II and Pen will appear eventually, thats what i do..
The only way to get items with the special mods is to craft them. If you're getting those mods on re-engineering then that's a serious bug that could lead to bigger problems down the road. As much as it sucks, you have to get it from crafting.
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That's why if you want PEN, OVER, SPR, etc you craft a pile of beams or torpedoes at mark II VR until you get that mod.
For things like Omni beams that you have to craft at Mark XII we're out of luck.
(Apparently the engineering duty officer crafting missions can get you gear with special mods too, but again if they don't arrive with the mod you'll never get it.)
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normal text = me speaking as fellow formite
colored text = mod mode
My character Tsin'xing