I easily adapt to slight changes, so I may not be the best person to ask. However, no, I do not find it AT all uncomfortable. Not in the slightest. in fact, of all the AR's I have, and in all the configurations they have been in, with all the optics I have and have used, the T31 on a TA51 mount on top of the SIR is my favorite so far.
There are weird quirks about it. For example, the TA31 I have is designed to be used with a 20" barrel mounted to a carry handle. I use mine with a 14.5" barrel, mounted to a flat top.
The TA51 mount puts the scope at the propper eye level when mounted direct to a flat top. I have mine mounted to a SIR which is slightly higher.
These "quirks" if you will are not really disadvantages as far as I see it. Especially if you know about them going in. If you do, then you just have to learn to work with them.
If you are like me and can easily adapt to new things, go for it, I doubt it will bother you in the slightest. If you are sensitive to changes, you may notice the slight raise in the scope. It may bother you. If that is that case, maybe think about the new RAS II which has many of the same features as the SIR, but allows the ACOGS to be mounted at their normal height with the TA51 mount.
BTW, no, you can not mount a ARMS #40 under an ACOG using the TA52 mount direct to a flat top. You can however, use the ARMS #40 behind the SIR and mount the TA51 and ACOG on top of that, Thats the set up I have currently.