I've been learning and experimenting with modes only recently, despite having played guitar for almost 11 years. In the past, I would use a "no-holds-barred, free-for-all" approach to writing riffs, and my instinct would tell me where to end the riff, or where the so-called 'home' note is.
Now, looking into the harmonic minor scale, I play E Locrian 13 (ascending-then-descending), the first mode of D harmonic minor:
1(E)-b2-b3-4-b5-6-b7. Even when I play it over a bass note backing track (E, E-octave), my head automatically fills in that I have to end my playing on Dm or D5 in order to achieve 'finality'. This also happens to me with other modes of this scale.
When I play E Super locrian bb7 (7th mode of F harmonic minor), ending on E feels very uncomfortable. Moreover, if I linger on F or its octave for more than a second, I cannot 'unsee' or unhear the apparent home note of F even with a backing track constantly playing E-E. I don't have this problem between natural minor and major.
Why does this happen? How can my head possibly know where the 'home' note is if I'm playing with a backing track on a different note? How am I instinctively reorienting a mode to the harmonic minor scale despite having no knowledge of modes till very recently? Can I train to avoid this from happening during my playing?