Can a customized GRCh38 .gtf file be used with any of the GRCh38 released patches? I got a customized GRCh38.79 .gtf file (modified to have no MT genes) and I need to create a reference genome out of it (for 10xGenomics CellRanger pipeline). I suspect that the .79 part is the Ensembl number, which according this ensembl archive list is paired with the GRCh38.p2 patch.

Should I use this patch's fasta file, or it would be fine to use any of the GRCh38 patches?
You can see the exact assembly by looking in the README file in Ensembl's genome download page. ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/README

As you can see the current assembly is GCA_000001405.25. Ensembl 79 uses version GCA_000001405.17. You can expect some differences between assembly versions. 

If you take a look at https://www.ncbi.nlm.nih.gov/assembly?term=GRCh38&amp;cmd=DetailsSearch 

You can see that 20,466,394 bp have been added since 17 -> 25. This is only about 0.6% change so I would guess there is not that much difference between these versions. However, if I were you I would use the corresponding version of Ensembl. Even better would be using the latest version of Ensembl, as not only the genomes primary sequence but also the positions of genes can change between versions (https://doi.org/10.1093/bib/bbw017).