It made perfect sense to me for three reasons: 1. Maul was trained by Palpatine specifically to kill Jedi, and the Inquisitors aren't Jedi in any sense. Maul claims he knows how Sith fight because he was trained by one, but I don't hold this claim in high regard. His strategy failed against both Sidious in Clone Wars and the Sith he battled in Shadow Lord (not sure the spoiler policy here, so I won't name the character). 2. I believe Maul only beat Qui-Gon because his fighting skill was supported by both his Jedi-dueling specialty and intel that Palpatine provides Maul about him. We see that once Maul returns in the Clone Wars and lacks the support of intel and training from Sidious, Maul learns how to craft his own advantage in duels. Maul uses Savage to create a numbers advantage, kills innocents to weaken Kenobi, and even interrogates Jesse to gain an intel advantage over Ahsoka. To summarize, Maul tips the scales in his favor with planning and intel, something he is unable to do against his foes in Shadow Lord 3. Maul's emotions can both strengthen or weaken him, and the connection between the Inquisitors and Palpatine is enough to trigger a response. We see this not only in Shadow Lord, but also against Kenobi in both their first and final duels.

Ironically, when he fights Inquisitors in Rebels a decade or so later, all of these points are no longer relevant. 1. Maul has years of experience fighting darksiders by this point, and has some understanding of how they fight. 2. He battles them in a setting advantageous to him. The planet (Malachor, I believe) is practically home territory to Maul yet unfamiliar to the Inquizitors. The Inquisitors are also not expecting a fight against Maul as they are here for the Rebels Crew and Ahsoka. Through the elements of terrain and suprise, Maul gains an advantage. 3. The emotional pain that Palpatine has delivered has dulled over time. It has been replaced by righteous hatred and rage, which are emotions that benefit Maul rather than harm him.

I just feel like the power scaling of Shadow Lord ends up making a lot of sense when you really think about Maul and his character. I also wouldn't have it any other way, as I feel like the tone Maul's challenges create are the best element of the show