I noticed during Shadow Ops every Sundays that there is a special base you will encounter the get more great prizes, but if you invade those bases you will encounter one special boss unit which are the rogue faction counterparts of Hero Units such as Nightshade (Black Widowmaker Prime, but since its a drone unit, she can't pilot those. Maybe those messages you'll see once if you continuously attack her until she defeated it looks like its from the Command Center), Hannibal (Mutoto's Right hand who controls a customized Warhorse with twin barrel cannon and a bulldozer blade on the front that similar to a Vanquisher), and Kronos (Which is a same Omega Hydra unit, but with different turret).
Official Rogue Faction Bosses
Nightshade - The Black Widow (Not a Rogue faction name, but a SF-sized Widowmake Prime)
Hannibal (Mutoto's right hand) - Warlord (A modified Warhorse with a bulldozer blade and two barrel cannon)
Kronos - Kronos Tank (an Omega Hydra with different turret)
Zachariah Kane - Unknown Crusade-like Tank
Now here's my ideas for the other Rogue Faction Boss units. Mostly RF Boss units are ground vehicles.
Krauser (Name idea for the Unknown Armored Corps leader) - Slayer Tank (A modified Legendary Mega Tank with a two rocket launchers that fires on aircraft which is similar to Hover Tank)
Shade (Name idea for the Unknown Corpus leader, but not the standard infiltrator soldier picture) - Corpus Stealth Tank
Smoky (Name idea for the Unknown Highway Zealots leader) - Zealot
Sasha Kalashnikov - Lokust
Sergei Kalashnikov - The Sickle Mammoth
Goro Tazaki - Ryu-Kai Legion (A modified Elite Legion with a Samurai armor)
Malachi - Sentinel Tank
Odin - Iron Walker
Heinrich von Kruger - Verkraft Hellfire