The original timeline was always sketchy, mainly due to fan interpretation and the design team not truly bringing the story together in a concrete way until the 3d era games. A primary example of this is everyone's belief that Scorpion became Sub-Zero's personal protector in the old timeline, which did NOT happen, as MK4 clearly showed. In MK4, Scorpion still believed that Sub-Zero was Bi Han, and that he somehow cheated death, and was directly responsible for the murder of his family.

All of the endings in MK1 - MK4 were only partially canon, meaning some but not all elements of a character's ending may happen and influence the next game. MK4 had about 3 possible overall outcomes to the story, based on character endings which can all be linked together to form one ending story. Examples of this include:

Ending Storyline 1 (Bad ending): Tanya - Reptile - Shinnok - Quan Chi - Scorpion

Ending Storyline 2 (Good Ending): Liu Kang - Kai - Sonya - Johnny Cage - Raiden - Fujin - Scorpion

Ending Storyline 3 (Mixed Ending): Jarek - Jax - (Good Ending) OR (Bad Ending) - Scorpion OR Sub-Zero

Irrelevant - Reiko - MK Gold

We know now, based on MKDA's opening, that the "Good Ending", linking all of those character's specific endings together, was canon. So that leaves us with a specific question - DID Quan Chi actually give Shinnok a fake? If he did, was he always planning to betray Shinnok? We ask that, because the new timeline clearly shows that Quan Chi is actually fiercely loyal and subservient to Shinnok.

Or did it?

Quan Chi is the proverbial roach infestation of Mortal Kombat. You kill him and he keeps coming back. MK9 diverted the original timeline, which means that although MKX is a new interpretation of MK4, it is so vastly different from MK4 that it cannot be compared in that sense. The events of the previous timeline's MK4 happened in Chapter 1 of MKX, but thanks to the events of MK9, the war played out very differently. We do not know for sure now if Quan Chi gave Shinnok a false amulet, as it seems that Quan Chi was permitted to use the amulet during MK9 (though that could be a continuity error, retcon or simply a design choice, since Raiden and Sub-Zero did not recognize or mention the amulet that Quan Chi was wearing during MK9).

Because of how differently events played out, we won't be able to tell until MKXI what Quan Chi's intentions were since, as we all probably anticipate, he will be back yet again. He may have been trying to utilize Shinnok to his own ends in this timeline just as he did in the first, but it is also possible that NRS completely retconned that aspect of the original timeline and made Quan Chi loyal to Shinnok this time around. Since both Quan Chi and Shinnok were obviously defeated by Earthrealm, we never got to see what Quan Chi's plan would have been had things turned out differently.

Quan Chi being a weak, old and powerless man...that I did not understand at all. Throughout the whole story, Quan Chi just appeared to be weak and tired. This was never explained.

TL:DR - Quan Chi seems loyal in the alternate timeline, but thanks to how events played out we never got to see what his ultimate intentions may have been.