Yes, we do support entering benchmarks without a standard or strand. The benchmarks will become course level based and are managed by the course editors instead of the admin user. We had done this for one of our managed TODCM sites. This requires changes to the config.php, unit template, search template, admin template and couple database tables. The actual source code is already in the open source package, the most important files are system/application/controllers/course/outcomes.php and system/application/libraries/unit/unit_os.php.
The problem is once you start with this setup there is no easy way to add strands and standards later. Basically, they are 2 separate template modules - one deals with learning-targets/benchmarks with standards and strands, the other one deals with course level benchmarks without standards. These 2 template modules are not compatible even though they use the same database tables. You can't begin with one module and switch to the other later. The fact is that the unit_os.php template module will assign all benchmarks to one dummy standard and one dummy strand. You could go into the database and reassign the dummy standard but this is a lot of direct database modification.
The one used in the open source package supporting strands and standards is system/application/libraries/unit/uph/uph_lt_extended.php, the other one is system/application/libraries/unit/unit_os.php mentioned above.
We are still in the process of documenting the template module parameters and I can send you what we have so you can look into the module parameters.
It looks to me your school needs good amount of customization work over the standard open source package and you should consider getting commercial customization and support from us. There are many advantages letting us to maintain the templates and configurations of a TODCM site, like guaranteeing all customizations will work for future TODCM releases etc. Please let me know if you need more detail.