Taking this right back to the beginning perhaps explains the problem best.
I got my X-Pro1 in late June 2012, probably from the second or third batch into Australia. Adobe came out with their ACR support for RAF soon afterwards, but my first few weeks were spent shooting OOC jpeg while familiarising myself with the camera. Once I started to process raw files with ACR I noticed that things weren't the best, but compared to SilkyPix (I use Windows, they were the only two RAF processors available at the time) there was not much difference, although SP seemed a bit softer and ACR more contrasty.
Then Corel got on the RAF train (September 2012) with their process in PaintShop Pro X5, and while worse overall, it probably best reveals why both early SilkyPix and ACR acted like they did. Below are two 100% sections of a photo I took at the time deliberately to highlight with vegetation and high contrast edge rendition I'd been noticing with ACR (and to a lesser degree with SilkyPix), and which many later called the "zipper effect".
The first is ACR, the second is Corel PSP X5. (Again, these are the first 2012 versions of RAF processing, not the current versions):
The Corel version perhaps shows the problem that Adobe etc with Fuji files, and the original dcraw showed a similar result to the PSP X5 version - spurious coloured pixels appearing along high contrast edges (note the lines between grille and white paint on the car and around the number plate, and the choppy edges of the geometric grille pattern against white plain detail; in fact anywhere there is a high contrast edge. If you compare the top edge of the door mirror you can just see the slight waviness in the edge of the Adobe version corresponding to where the rows of spurious pixels occur in the X5 version, again probably confirming default filter application designed to smooth edges.
My guess was (and still is) that both SilkyPix and Adobe tackled this with a default addition of noise reduction (more heavily so in Adobe's case), and compensated for the NR's softening of detail and loss of colour by adding a hefty dose of saturation and sharpening. The spreading of colour in the two sticks embedded in the ground further attests to the likelihood of NR having been applied - the green/yellow colour of the grass spreading has nearly killed the brown in the highlights.
As mentioned, I tried dcraw in command line form when Mac forums started mentioning it as being the basis for RPP & Iridient, and it gave a similar result to Corel's demosaic, but Dave Coffin then responded quickly to criticism and changed his demosaic algorithm to give the clean, sharp rendition that is with us today as the basis of programs such as Photo Ninja, Iridient, RPP, LightZone, Photivo, Helicon Filter, etc etc. Corel took a lot longer to respond, and still hasn't quite got there with Aftershot Pro.
Adobe (and probably SilkyPix) on the other hand, seem to have stuck with their original algorithm and simply refined the degree of default NR, saturation and sharpening applied to reduce the outline and spreading effect of the original. This would probably also explain why Adobe ACR/LR/DNG files in particular can react so nervously to post sharpening, sharpening apparently already having been applied by default during the demosaic.
Until someone from any of the companies mentioned actually comes out and publicly states that this is not the case (and they haven't in five years), then I'm inclined to stick with the above explanation.
As such ACR/LR/DNG is basically flawed in my book, and while many might think their results are good enough, my personal quality standards (and those of many others) won't permit me to use ACR for any commercial job. One never knows how the final image may be used, at what size and with what enhancements, and as such it is the professional's duty to provide the best possible image to the client, not one that may - or may not - be "good enough". Iridient's X-Transformer is definitely a viable demosaic alternative to those who feel welded to Adobe and the ease of ACR/LR, just be sure to properly tune the base settings (to their credit Iridient do listen and have already changed the defaults at least once).