Quartz.NET can be instantiated on a per-application basis (web farm configuration mandates number of schedulers). You can safely run multiple schedulers if you have your jobs backed in a database and you have Quartz.NET configured in clustered mode (and clocks synced naturally).
The main concern is to the application pool handling prior to IIS 7.5. Without constant checks your application worker can get recycled and your scheduler will be down until someone issues a web request to fire up the application pool again. IIS 7.5 has the new feature to keep application pools running all the time.
Otherwise there should not be a big difference between the two models.