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It doesn't seem like it should be related to Linux if everything else works. I just double-checked and I am also able to apply the LC version of your patch, just not the main file.
I looked at the Play Store page and I'm not sure that it's available on plain Linux (Ubuntu). There are entries...
I've tried Marc Robledo's online JS patcher and flips. I'm using the Linux version of flips, but I seriously doubt my OS would impact the online alternative.
My ROM
CRC32: 81069d53
MD5: 219b2cc64e5a052003015d4bd4c622cd
SHA-1: 0f8670a583255cff3e5b7ca71b5d7454d928fc48
I get an "invalid patch format" error when attempting to use your ips file. I was able to apply the PTCG Neo hack successfully, which suggests that this issue was not user error.