This isn't necessarily true. Other characters have already commented that her system is actually brilliant. For example if there is a task that takes 20 people to run with a standard system, she was the one who made a system that cut that work down to 10 people... And then proceeded to run it by herself.
One engineer being able to outperform 10 engineers is a bit exaggerated but not necessarily unfounded. Difference in skill and work management can really be that massive, and if she's truly a one in a million genius, she was probably extremely undervalued and even now being underutilized at her new company. The best engineers get jobs at some of the biggest companies making 6 to even upwards of 7 figures, working on projects that completely revolutionize the world. She just needs to have her work and talent recognized by the right people.
Supposedly she left proper documentation behind, so it shouldn't take more than a few days, a couple weeks at most, for a competent engineer to adjust. No one is complaining about the system, so it probably isn't the problem.
In the end, this manga is just another wish fulfillment fantasy of another flavor. This company will slow burn to hell and the readers who have all felt being underappreciated at their work will savor every moment of it.
She was extremely undervalued, but she wasn't underutilized, she was mismanaged and overworked
She left some documentation behind, but it is clear that that's not enough to train people on how to deal with her system, no one is going to badmouth her software because it is a genius application, however it is a fact that it is a tool that only she knew how to properly use, and no one else, and that's the problem, that she made a tool for a company that only she can properly use
I guarantee you they will end going to her and ask her to train the engineers on how to deal with her system, which is something they should have done from the start and never did, and that's the end game of this manga
That's the whole reason why she ended conveniently working as a private tutor out of all the things she could have done after being fired
And is a solution they only can use, because she is still alive, she is still available, and she ended up working as an educator, but the moment she declines the offer, they will end back in with a system that no one knows how to properly use
But think about it, this new asshole manager gets fired, and you are hired as his replacement.
The first manager approved the making of an in-house software, and never worried with making sure to have any backup plans, they either assumed their main dev was going to be in there for life, or that the thing she made was easily accessible, but thing were great for him, at the expense of this one genius woman bearing all the burden
The second manager then came in, and fired the main dev and half of her team, the other half is already in the process of quitting, so none of the original members with all their experience will be around by the moment you arrive, he has also failed to recognize that the in-house software is not something everyone is familiar with, so as he drops out with a golden parachute, he is leaving you with this mess, and pretty much a need to build back a new engineering section
Now it is your turn, you have a department that is failing away, everyone working there is miserable, they are mostly new hires, the department is eating resources, its level of production dropped in half and is affecting the whole company, it creates bottlenecks daily, but the team size grew up to 12 people, a size that the company can't really affort, but it is either that or halting operations entirelly
You don't find a new genius engineer to come and save you, head hunting has failed, there's no Satou 2.0, who just so happens knows exactly how to keep this running optimally.
You did found a 1 in a thousand guy, but you needed a 1 in a million guy, if you abuse the shit out of him... you can reduce the team to 8... maybe 7 people, not really a solution by anymeans
The main deus ex machina, the protagonist, is also gone, she can't be rehired, nor can she be reached to train a new team, no one else in the world actually knows the ins and outs of the in-house software, all you have left is the last minute document papers this super genius woman made, and this is what allowed the team to make it this far
What do you do? if things keep going like this the company will start acquiring lots of debt, and you can't really keep increasing the team, you just came out from the previous administration that downsized the company in order to avoid failing in the red
I am not saying you shouldn't insist on keeping the brilliant inhouse software that no one knows how to use, but..