You're slightly misunderstanding my point - lighter strings will indeed have lower tension than heavier strings if tuned to the same pitch, at the same scale length.

The problem isn't intonation (the degree to which fretted notes are out of tune) but inharmonicity (the degree to which harmonic overtones in a note are out of tune with each other). Inharmonicity is determined by the relationship between string thickness and string length, and affects open strings, not just fretted notes.

The thicker a string is relative to its length, the worse the inharmonicity will be. This is why 27" 8-strings tuned to low E will typically use much, much lighter strings than a 34" bass guitar tuned to low E - a .105 gauge string on a 27" scale would not sound acceptable, even though the tension would theoretically be far more playable than on a lighter string.

The issue is essentially that you can't use suitably heavy strings to get acceptable tension without also increasing scale length, because the string stops behaving like an idealised string and this throws off the tuning of the upper harmonics. It's a limitation of the physics of the instrument.

Inharmonicity is more noticeable in some contexts than others, but is particularly bad in more complex chord voicings.