that's right, many (but not all) 3D applications, and even video apps, think and work in this manner: if there is an alpha channel in the image (for example if it is a 32-bit tiff instead of a 24-bit tiff), then it is assumed that the 8-bit alpha channel is holding a mask of some sorts, and that it should be used as a transparency mask. (or opacity mask, whichever you look at it). Carrara does the same now, but it wasn't always that way, i.e. in the past the shader in Carrara had just a transparency channel which you had to explicitly feed with the mask, whereas now in v5 you can send a picture into the color channel and it will check if there's alpha and if so then it will use it for transparency.

Managing the alpha is one of the things we focus on in PD Pro, and we recently also added a few free plugins to the $19 lite edition, PD Particles, through the cooltools #1 collection for PD Particles, containing tools like Store alpha, paint on alpha and grow and shrink alpha. There's also adjust, blur and other alpha (invert alpha) tools in the menu of PD Particles.

In Bryce you will load the transparency mask separately, so it's just a greyscale image. Note that if you have an image which holds alpha already, and you want to use that one, you can usually find tools in your imaging program such as PS or PSP (and of course PD) to extract the alpha and save it as its own greyscale image.

One think that becomes important too is that the transparency mask be controllable, with regards to adjusting the value, brightness, and especially gamma and contrast, so you can make sure that black is indeed totally black (opaque) and white is totally white (fully transparent). Some imaging tools will offer one-click solutions like 'adjust dymaic range' so as to make sure that the minimal and maximal values possible are indeed reached.