The "zip inconsistency" linked is not a problem of the Zip file format specification. The goal of the zip format was never to provide a tamper-proof cryptographically secure binary package. Whoever uses this structure for some more security-wise complex demands is responsible to make sure that the security assumptions he needs are respected by the code he implements. One simple method were signing the resulting archive, then no modification is possible, and therefore also isn't possible adding a second entry with the same name by the attacker.

I really don't care about HTTP headers or Reed-Salomon, as they are completely irrelevant to the Zip format designed in eighties for very specific purposes then (being fast on the floppy disk and 4 MHz 8088 processor, allowing to recover as much as possible from the floppy even after the floppy disk sector failure), I just claim, through the whole conversation here, that the Zip format is not a bad format for having a central directory and the metadata outside of it too, and I gave my arguments for that. NTFS also has some metadata on more than one place and it's an intentional design decision solving real problems: in Zip case allowing for fast access of the list of the files in the archive but also easy recovery of the single files when some part of the archive gets corrupted.

I also claim that the Zip format is not in any way "bad" for not making impossible per the archive format design and specification of having the two identical file names in the archive. I can even imagine use cases where exactly allowing that is/was beneficial.