Are all packages referenced in JEDEC JEP95?
Not necessarily. This is just a standard document compiled and published by JEDEC. This probably covers around 98% of the commonly used packages, but may not be a comprehensive list of all packages used by every manufacturer.

For an IC manufacturer, there is a great advantage in using a JEDEC standard package, because of existing support among IC manufacturing equipment:


Computer Aided Design tools
Internal Leadframes
Wire Bonding equipment
Epoxy molding die forms
Automated Test Equipment Handlers
Tape and Reel


Furthermore, the manufacturer's Quality Assurance department will have already compiled reliability data, and will have tested and approved the package. (At the company where I work, getting QA approval for the final package is sometimes an element that gates production release of a new product. That only applies if it's a package our company hasn't used before, not whether it is a JEDEC standard package. But we have no reason to restrict ourselves to only using JEDEC standard packages.)

There are also solid marketing reasons to stick with standard package sizes, since the customer's CAD / PCB layout tools typically already include JEDEC standard packages. Whereas if the IC uses a non-standard package, then the customer must do some PCB library work to create a PCB footprint that can be used with the IC. Some manufacturers provide suitable footprint drawings, but sometimes all that is provided is a drawing of the IC package itself, and it is up to the customer to make allowances for wave soldering / reflow soldering and other PCB assembly requirements.

So most IC packages typically will be JEDEC standard, since that's usually easiest for the manufacturer and their customers. However, sometimes an IC manufacturer has a compelling reason to use a non-standard package, such as improved heat dissipation, or minimizing space for a high-volume customer (consumer electronics, cellphones, etc.), high voltage isolation, high speed, or other reasons specific to an application.