The filter factor is actually a number divided into the exposure index of the film to determine the final exposure. This was handy when using a handheld meter. For instance, a filter factor of 4x used with ISO 400 film would mean you would adjust your handheld meter to read 100 instead of 400. For those of us who are mathmatically challenged, that gets confusing. It's also unnecessary (and sometimes inaccurate) when using the cameras build-in meter and reading through the filter.
You have the right idea, since you are determining the increase in exposure in stops instead of filter factors. If you're using a handheld meter, it's good to make a chart of the exposure increase of each filter you use and attach it to the meter.
When using a filter that increases exposure beyond the recommended range, you have to compensate for this by increasing the exposure. If, for instance, a certain film has an exposure index of 400 at shutter speeds from 1/2000 to 1/2 second, you will have to increase exposure if you use a shutter speed longer than 1/2 second. This amount of compensation varies over the period of exposure. The exposure compensation is usually on the information packed with the film or it can be found on the manufacturer's website.
If I'm understanding your question correctly, it has to do with this compensation in exposure. It can be due to using a filter or simply due to the low level of the light. Your depth of field will be affected only if you compensate by opening the aperture of the lens as opposed to using a slower shutter speed. Once you're into shutter speeds of 1/2 second or slower, you're out of the realm of stopping much action so increasing exposure by adding time is usually a reasonable act.
You also indicate you "may have to forgo definition in your ground level scene or at least try and equalise to a degree". You should consider a graduated neutral density filter. This filter is made specifically for such purposes. With the graduated filter, you make your meter reading of the "ground level" subject you indicated and use the filter to hold back the brighter sky. It's an in-camera way of burning in large bright areas within the frame.
Jeez...I've taken your straightforward question and babbled on too long. I hope my response doesn't confuse you further.