There is a popular feature request that would probably capture this -
http://ncrunch.uservoice.com/forums/245203-feature-requests/suggestions/5652744-separate-ncrhunch-project-configuration-from-user.
The original idea behind the 'Ignored Tests' feature was for it to be used to specify tests that wouldn't work with NCrunch. Such settings were ideally shared between team members as it would be annoying for them to need to each re-flag the tests that NCrunch couldn't run.
NCrunch does have a user only file (ncrunchsolution.user), which is basically a binary file containing non-critical configuration such as tool window layouts and the currently selected engine mode.
See here for a list of files created by NCrunch and what these files represent.
The Engine Modes (with their filters) are stored in the shared solution configuration file (ncrunchsolution), but the currently selected engine mode is stored in the local file (ncrunchsolution.user). This makes it possible for you to have your own Engine Mode (or set of engine modes) that you use for your work style - and others can use this if they choose to.
The main problem with NCrunch configuration is that where this configuration should be stored and how it should be applied seems to depend very much on how people are using the product. This makes it impossible to create a static design that can cater for all needs. The ideal solution is to introduce additional complexity into the configuration system to allow many of the settings to be specified on a user or team basis, with support for inheritance etc. I'm fairly certain that this will be introduced - though at this stage I can't promise when it will happen.