I download symbols and footprints from the component supplier into a project’s library to go faster but I realized that many of the standard components footprints are slightly different in KiCad, like for example the SOT-23-6 so my question is: is it better to stick to KiCad footprints or just use the suppliers footprints?
If the footpritns you download from a part manufacturer are good enough for your usecase then the footpritns in the official lib are good enough as well 
Reasoning: Footprints are not that critical until you start to yield optimize your manufacturing process
This does not mean footprints are not critical at all. But i would assume that the manufacturer has a similar quality standard then the official lib. For reference especially footprints for standard packages are derived from industry standards in the official lib.
If you hand solder than any footprint with close enough pad size will do as long as you have enough space for getting your tools in.
If you hand apply solder paste (even with a stencil) then the variation of this process will be much higher than the differences between reasonably well-designed footprints.
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I had used the KiCad library and had help contributing with new symbols/footprint. I think those are more stable and reviewed by the community and also use the same orientation for the pick-and-place file generation (automatic assembly process).
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But if you are using because they provide some special component or fields with “manufacture part number” (to help you with the BOM), it is a good advantage.
Whether a footprint is made by a “component supplier” or by “KiCad” is not relevant in deciding what to choose. Solder paste is, well paste, and it flows during reflow 
and there is room for different sizes to fit the same purpose equally well.
What should count is the quality of the footprint.
I do not have much experience with this, as I use KiCad mostly on a hobby level. I do remember a story I read about this and what I remember from that story is that most differences have negligible impact (as long as the parts fit of course) except for round corners in the solder mask. Round corners are good, because sharp corners tend to retain a changing amount of solder paste and the variations in the amount of solder paste deposited on the pads which can lead to quality issues. For the same reason the openings solder stencils should have slanted sides (trapezoidal cross section) with the wide part on the underside to more easily loosen the paste from the stencil.
There are even complete magazines dedicated to the production of PCB’s. You may find more ( better?) info there.
https://www.startpage.com/row/search?q=pcb+magazine&l=english
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