This is the exact reason many sets are 45-65-80-100. The D string, being farther from a flat pickup on a radiused fingerboard, has more mass for its pitch to make sure it induces the same strength of signal as the G and A strings. Similarly, the E string is lighter, because a lighter string is more flexible, which means generally more overtones so the tone is similar to the A string and not thumpy.
On modern 5-string basses, the crown radius is usually flatter, so the D string does not always need to be thicker to have the same tone as the G and A strings, and modern multi-wrap construction means the E string can retain more overtones than older string technology.
All of this means it is good there is diversity in selection of bass strings for each player's requirements and desires.
