It is said on page 136 of the Beta rules that "Weapon customisations may only be applied to a piece of equipment that is part of the Standard Regimental Kit or a favoured weapon of the soldier's Regiment. Guardsmen never have sufficient exposure or training to safely customise more specialised weapons."

Can Specialist Gear be therefore customised, or not? Can a sergeant customise his Chain Sword, a Ratling his Sniper Rifle, or a Storm Trooper his Hotshot Lasgun?

Rules seem to indicate No. However it doesn't make much sense. In addition, the armourer (trade) skill allows me to build a plasma gun from scratch as long as I have the materials and schematics, so it shouldn't be impossible.

In our group we count that specialist gear as part of standard kit gear, because if you're a weapon specialist and favored regimental basic weapon is a bolter, but you instead of choosing that decides you're supposed to be a flamer… it doesn't make sense that you've been trained enough in that to make the same changes as you would your other weapons, some of which you probably used less than your flamer.

I think that Weapon Customization should be avaiable for all weapons. If you want to risk making your once-in-a-lifetime melta gun that got though a administrative hickup an unreliable piece of junk, go ahead.