Do you have a personal bottom limit, or do you even like the lowest power chord available on a fiver (F# over an open B - BTW do you Anglophone guys call this a "double stop" even if technically you're only stopping one?)?
My personal lower limit is E2 over A1 (the lowest available, not inverted, A-fifth on a standard-tuned bass: 55+82.407 Hz fundamentals). This is regardless of strings used - I don't like anything lower even on piano; it's actually a matter of fundamentals and lowest overtones, not "tone"; physioacoustics tells me the lower a vertical interval is, the closer frequencies are relative to critical bands:
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Masking occurs of frequencies "too" close to one another, and the brain attaches a feeling of roughness to these overly narrow intervals. Please note that my still-kosher A power chord has its fundamentals fall within the same critical band: in other words it shouldn't work but does, for me. That's why I don't discount your experience either; your brain may not find it particularly unmusical when two tones are masking each other because of proximity, especially when everything else is in order, harmonics-wise, above the deep bass area.
My position on the thread topic is, you have to either keep the two bass-lines (hyphenated to remark that one won't have typical supporting duties) well spaced from one another, or you have to through-compose, and plan unisons, or temporal slotting (actually always a good solution), beforehand. Pick your poison.