I agree with you exactly about both the whistles' endings and the uneven cadence of the chuff, as I stated before either on this or the general net. I also don't like the rotation of the chuff sound between different files. I think BLI went off the rails on these "features", possibly with the misguided intention of making for greater realism. AFAIK, these cannot be adjusted, so I have also thought in terms of a replacement decoder. The expensive 4-12-2 I bought, while beautiful to look at, not only had these problems, but the chuff was not, and could not be, sychronized with the drivers; for a 3-cyl engine, the gear ratio they chose is incompatible with the Paragon 2/3. This made me angry at first, then I sat down and installed a TCS WOW, which gets sync from six tiny disk magnets and reed switch I installed on the front driver.
I recently saw an in-depth demo of the Tsunami 2, and believe it has great sound; however, it has no sync wire for chuff input. You lose your positive chuff sync, having to use the BEMF signal, which is difficult to make do a good job on startup/very slow speed. I have had good luck with the WOW and the Loksound. Or you could use the original Tsunami (not a good sound for an articulated above 25 mph, tho).
Be aware that if you install a WOW or original Tsunami decoder in a BLI, you cannot use the pickup they use, which is a magnet installed in the flywheel. This puts out too many pulses per rev (the gear ratio divided by 4 for 2-cyl engines). BLI does it by using a countdown circuit internal to Para2/3. So a magnetic or mechanical commutator will be needed for positive sync, as I had to do with my 3-cylinder UP. IIRC, the Lok4 also has a programmable countdown, but doesn't include 6, so this didn't help with my UP.
I plan to refit some of my other BLI Para2/3's with WOW or Loksound, to get away from the corny sound.