You should select the average tolerance for each chip package. Choose vendors that fit into those tolerances but have your own personal tolerance that you can round up or down to fit into your tolerances. 

Example: 

If you have tolerances like this - +/- 0.10, +/- 0.15, +/- 0.20 then the average in +/- 0.15. 

You can take the 0.10 and round up and the 0.20 and round down. 

It's a fact that every component manufacturer tries their best to deliver their packages in the Nominal Material Condition and then the tolerance is unnecessary. But to be on the safe side, create an acceptable tolerance table. 

Then you need to deal with manufacturer's that have slightly different package dimensions. 

And the Package Height is another factor. 

Here's a Chip table with common dimensions. Avoid using manufacturers that have different dimensions or create a special footprint for them. 

 

I wouldn't bother too much about different tolerances. 

If a footprint works for one tolerance, it is very likely that it will also work for another tolerance. 

For sizes of 0603 and smaller, however, I would simply ask an assembler for a well-functioning footprint, anyway.

Anyway, it appears that the tolerance does not make a difference in the footprint names (or their descriptions)... so if you made a footprint for an AVX cap (1812 with X7R dielectric), and then made another footprint for AVX cap (1812 with COG dielectric)... even if the height was the same, if they have different tolerances, the pad sizes will be different, but the footprint name would be the same.

If a person was to create multiple 1812 cap footprints, and the only thing that was different was the tolerances... you might have 4 mils longer distances between toes, 2 mils shorter distance between heels, and 8 mils greater pad width.

So if you DO actually have multiple footprints for the same SMT cap size, how do you differentiate between those footprints? You'd have to give then a different name? that uses the pad dimensions maybe?

Regards,

Chris