NCrunch doesn't support the use of MSTest deployment resources through the testsettings file, so no files that you specify here will be copied into the testing workspace (as you've described). There are two ways you can work around this:
1. Declare the files to be copied by using the DeploymentItem attribute on your tests, instead of in the config file (as NCrunch does support this)
2. Reference the files in their original location within your solution, using relative paths. Provided you have included the files within the NCrunch workspace using a .proj file, or using the 'AdditionalFilesToInclude' NCrunch config setting, the files should exist underneath the NCrunch workspace (which in your case is at C:\Users\user\AppData\Local\NCrunch\12884\98\). NCrunch will always store the files with the same relative path as they would be within your normal solution, so you can access them by referencing upwards from your test 'Out' directory ... for example: ..\..\..\ResourceFiles\myfile.txt. If your code is fully dependent on the files existing within the 'Out' directory, you could rig up an extra step in the test to copy the files there.
I hope this helps.
Cheers,
Remco