Just a note that this is not correct. There are many formats of bitmap file, including those with alpha channels. The catch is that those such formats are not commonly encountered on Windows, and most bitmap editors won't edit or deal with them correctly.
When you want to edit a texture, TGATools2A is the software you want to open up the .ace file in. You can get TGATools2A from an Ace-It install. Once you open the .ace file in TGATools2A, immediately save it as a .tga file. The .ace format is largely MSTS-only, but the Targa format is more utilitarian and understood by more software. As @pwillard pointed out, TGATools2A will let you edit the color and alpha portions of the texture separately. Or, you can open the .tga file in software like Photoshop and edit it directly.
Be aware that you cannot just "add alpha" to any texture and expect it to work on any model. It is certainly possible to "alpha out" parts on a model, and you can add an alpha channel to the texture to do it, but the shape file may also have be modified so as to utilize the alpha portion of the texture. Since you are intending to just fix the alpha that was already there, and the shape is already configured for it, that doesn't apply here. But it's something to know going forward.