You can control the alpha component for any color attribute on a custom node separately by scripting.
The custom node factory creates a separate float type plug for any color type parameter, using the same name with A appended. The resulting attribute layout is as follows:
input (color compound)
inputA (float)
The A plug is magically connected in Maya for common cases, but can otherwise be set via scripts to values other than zero. This will be respected upon translation.
Connections of this plug to any other node are not supported.