Still not sure I'm following you.
setColorMod and  alpha are in base_render_osystem.cpp:153 and do just what they're supposed to, if I understand correctly.
They set the renderer's color mod attributes (which haven't been ported to TransformStruct and I'm not sure it would be useful), not the sprite's.

void BaseRenderOSystem::setColorMod(byte r, byte g, byte b) {
	byte alpha = RGBCOLGetA(_colorMod);
	_colorMod = BS_ARGB(alpha, r, g, b);
}


Are you perhaps suggesting we move those to a TransformStruct?