Applause all around, except for the legibility fanatic who shoots angry looks. A lean tool that integrates with existing tools and workflows is chosen, and everyone loves it. The right projects are selected, and the most qualified people are working on them. The company has a promising future ahead of it.
The second decision is successful because it follows the Lean principle: The PPM tool should not increase the organization's legibility more than absolutely necessary. Anything extra would be wasteful. The decision also reflects that the more information you gather, the more likely you'll lose focus and get bogged down with insignificant details.
Maybe most importantly, the decision to not standardize so many tools and processes may actually be the reason for a good chunk of the overall productivity. The various solutions and workarounds that were never part of any corporate guideline and which may even look eccentric or stupid to the central planner, are likely what people choose to use because they simply help them do their job more efficiently. Local solutions forged by local knowledge.
Put differently, employees are happier when they have a certain level of control over how they work. In turn, they are more productive, and this productivity often more than offsets the promised gains in productivity achieved by standardizing tools and processes.
Yes, a certain degree of increased legibility, that is a better visibility of your portfolio is a sensible goal when introducing a PPM tool. Just because digital technology makes increases in transparency easy and attractive, don't let that blur the real reason for actually doing project portfolio management and don't underestimate the downsides of increased legibility.