I did a little experiment with the sub with and without polyfill. But some preliminary facts about my setup...
My Alpine sub requires 0.85-1.50 cuft net sealed, with a recommended volume of 1.17 cuft net. My current sealed box gives the sub 1.10 cuft net, virtually the recommended volume. I tested the bass output using some test tones and some bass heavy songs. This is what I found...
Low freq (30-50 Hz) output did not differ much between polyfill vs. no polyfill. Both setups played low frequencies very well. But at the higher bass frequencies (60-80Hz), the bass had more punch without polyfill in the box.
I don't have any scientific explanations for this, but from my experiment, I found that polyfill is not needed, in fact, hurts bass response, if the box is already built to specs. If the box was made much smaller, maybe polyfill could help, but I'm not sure. For now, I'm not using polyfill for my current setup. Hope that helps!
It will depend on the box, the sub, etc. It's interesting to hear your results, but there are way too many variables to say that it will always sound worse or always sound better.
I would recommend trying different amounts of polyfill, as packing it tighter or looser will likely affect the results.
Anyway, here's your explanation...
With a sealed box, generally the larger the box, the lower the sub will play. The compression of air inside the box creates a high-pass filter of sorts, and the smaller the box, the harder the sub has to work compress the air within to play those deep notes. It's not uncommon for a well-built infinite baffle set up (basically free-air with no enclosure at all) to play loud, clean, and flat down to 15Hz or lower.
Anyway, when you added the polyfill, in theory you tricked the sub into thinking it was playing in a larger enclosure than it actually was. The result is (theoretically) the ability to play a bit deeper at the cost of the upper sub-bass range. Sounds like the change in the upper range was more noticeable than the change in the lower range for you.
If you're interested in an experiment, try the opposite. Use no polyfill and put something in the box that will reduce the internal volume (like a brick, block of wood, etc). You'll probably notice even less deep bass but the upper range will be more pronounced, though not not necessarily in a good way.
In the mid 90s, the Kicker Solo Baric subs boasted their super-small sealed box requirements (I want to say .8 cu ft for the 12" but I could be wrong). In that size box, they could play insanely loud, but were 'buzzy' (all upper sub-bass) and didn't go deep at all. Once you bumped that box size up, they actually sounded quite good.