The biggest difference between a packaged drive and a standalone "custom" unit is the time it takes for you to obtain one. A "custom" drive can be several months between order and receipt, while a "packaged" one can be arrive in as little as three weeks.
The standalone is a custom-built unit that exactly matches your specific application requirements. It may or may not be modifiable at some later date to something else without significant reprogramming and/or additional components.
The packaged version contains all the hardware and software that is most likely to be used - either on an industry application basis, or on a power/speed basis. You pay for the whole lot, but only the items contracted for are enabled by the drive vendor. Packaged drives tend to be sized for either NEMA or IEC "standard" ratings (depends on the drive vendor).
The "packaging" does not include a specific motor. It's just the drive, with typical set points for thermal curves, pre-start requirements (like maybe external lubrication or fan), and ground protection. Additional I/O points may be available for monitoring vibration and/or other items - depends in part on the drive manufacturer and in part on the drive rating (e.g. not likely to have vibration sensors on a 100 hp motor, but will almost certainly have some on a 1500 hp machine).
The "software" is the logic for the drive, and the "pre-set" values in the memory registers for operating limits. Even though all the "typical" software is present, only some items will be allowed; others will not, depending on the way the drive was purchased.