Markdown was designed to be able to be read as text with minimal distractions.
Its key design goal is readability – that the language be readable as-is, without looking like it has been marked up with tags or formatting instructions, unlike text formatted with a markup language, such as Rich Text Format (RTF) or HTML, which have obvious tags and formatting instructions.
A link like this: [Markdown] is easier to read than [Markdown](https://en.wikipedia.org/wiki/Markdown).
It certainly doesn't matter to people reading but not editing a post on SE. However, when editing a post, using numbered links instead of inline links helps maintain the flow of the text for the person editing, and detect and correct grammatical errors if any exist, since only a single bracketed number needs to be skipped, instead of multiple words in a complex syntax (scheme, domain, path). The point of links is as an aside, or to provide additional information at the reader's discretion. It should be the reader's choice whether to follow up on that information or not, not the author's choice to force the reader to deal with it as they're reading.
Part of the change is from this:
[NASA is testing hydroxylammonium nitrate in space]
(https://en.wikipedia.org/wiki/Green_Propellant_Infusion_Mission). Due to its
[higher specific impulse and higher density]
484591_gpim_factsheet.pdf) it is expected to perform 50% better than standard
propellants. And it can be allowed to freeze, [hydrazine must be kept liquid]
on-a-spacecraft-is-it-always-kept-as-liquid-or). [LMP-103S has been tested]
(https://space.stackexchange.com/a/9679/4704) gets about [30% better
[NASA is testing hydroxylammonium nitrate in space]. Due to its [higher
specific impulse and higher density] it is expected to perform 50% better
than standard propellants. And it is allowed to freeze whereas [hydrazine must
be kept liquid]. [LMP-103S has been tested] and gets about [30% better
The former has so many embedded links it's impossible to read while maintaining a flow. It looks like code. The latter can be read very easily. It looks like English. An inexperienced editor might be put off from editing the "code" version, so their valuable input is never gained.
Changing inline links to numbered links should not be a reason for editing a post. But if you've found other issues that could be improved, I have no problem with adjusting the link style as well at the same time. Changing the link style at the same time as fixing other issues should not be a reason to reject an otherwise good edit.