Well, first of all there is no problem with encoding low frequencies here (we do all the time! like the fact that the notes are not all played at the same time...).
What you feel is parts of your body resonating (because the low frequency sound is exciting modes of your body). This is unlikely to happen at high frequencies, partially because it would necessarily be much smaller parts of your body (see [0] for a diagram of typical body resonance frequencies) which we probably don't feel and because attenuation of sound greatly increases at higher frequencies (for example, see [0] for air), making it likely impractical to excite any such modes. My guess is that you might cause some tissue damage if you had significant ultrasonic excitation in your body (see [2] for something that may or may not be true...).
You hypothesized about tissue damage from ultrasonic excitation, so this tangential post may be of interest. Tissue damage from ultrasound is an intentionally-caused phenomenon being used (and experimented with) in some non-invasive medical procedures, where focused energy can locally ablate a tumor for instance. HIFU, high-intensity focused ultrasound, is the technique: http://en.wikipedia.org/wiki/High-intensity_focused_ultrasou...
What you feel is parts of your body resonating (because the low frequency sound is exciting modes of your body). This is unlikely to happen at high frequencies, partially because it would necessarily be much smaller parts of your body (see [0] for a diagram of typical body resonance frequencies) which we probably don't feel and because attenuation of sound greatly increases at higher frequencies (for example, see [0] for air), making it likely impractical to excite any such modes. My guess is that you might cause some tissue damage if you had significant ultrasonic excitation in your body (see [2] for something that may or may not be true...).
[0] http://physics.stackexchange.com/questions/37543/does-the-hu... [1] http://www.kayelaby.npl.co.uk/general_physics/2_4/2_4_1.html [2] http://www.tovatech.com/blog/4376/ultrasonic-cleaner/ultraso...