A couple of things:
1. Unless we are talking a very small machine 45mm t-slot is very small
2. Tapping the extrusion isn't the norm. Depending upon how things line up you may have a hell of a time doing a good job.
For a little more highly biased info:
1. I really don't like mounting linear components directly to most T-Slot extrusions. In my mind you will be better off bolting to thick solid paced of aluminum bolted to the t-Slot. You will then have a flat surface to drill and tap to your hearts content. The more you expect precision wise the worst the t-Slotted extrusions are.
2. I don't understand your pictures.If you really want to use T-slot the part functioning as your gantry beam need to be rigidly bolted to the uprights. There needs to be the use of gusset or other reinforcements
3. A gantry beam is unsupported between uprights. You need to consider this when sizing beam size. Beam cross sectional area will vary based on that distance to span