In your Daf Insights you have the following:-
>>Moreover, the fact that the Gemara permits one to peel barley on Shabbos implies that the barley has not yet been brought to the silo, because barley is brought to the silo only after the husks have been peeled off. If, however, the barley has not yet been brought to the silo, then clearly the barley has not yet undergone the procedure of Miru'ach and has not become obligated in Ma'aseros. When one peels the seeds of barley on Shabbos into his hand, they should become obligated in Ma'aseros at that moment, since the act of peeling is the "Gemar Melachah," the final processing of the barley. Ma'aseros, though, cannot be separated on Shabbos. Why is one permitted to peel the barley on Shabbos if he will not be able to eat it since he cannot separate Ma'aseros from it on Shabbos? The barley should be Muktzah.
(a) TOSFOS (DH v'Im) and TOSFOS RABEINU PERETZ explain that there are two different shells around the kernel of wheat. There is a thin shell which lies directly on top of the kernel, and there is a thick shell which houses the kernel and its peel. When the Gemara (12b) says that one may not roll ears of wheat, it refers to wheat within both coverings, the outer husk and the inner peel. Rolling the wheat in order to remove the outer husk is prohibited because of Dishah (mid'Rabanan).
When the outer covering was separated from the seed before Shabbos, the seed may have been in the silo (after Miru'ach) and thus Ma'aser may have been separated from the barley before Shabbos. The barley which one wants to peel on Shabbos is not Muktzah since Ma'aser was already separated from it. The seed has only the thin, inner covering left over the kernel. One is permitted to peel off that inner covering on Shabbos. (The removal of the inner peel is not considered Dishah, just as the removal of the peel of a fruit is not considered Dishah. Dishah involves the removal of the container of the produce (such as the outer husk). The peel does not contain the fruit but merely protects it.)<<
I do not understand this answer as the question raised by the Gemoro specifically relates the question of a 'seeming' contradiction where you can do something (preparation of food for Shabbos) which is permitted, yet on the other side l'inyan maaseros it is forbidden.
According to the conclusion of the sugyah, (at least the way I understood it) once you have overcome the Shabbos 'problem' (maleches machsheves) the aspect that needs to be determined is the masseros. What happened to the Muktzeh problem. If these foods are subjected to giving T & M then they should be muktzeh??
The Gemara is not addressing Ma'asros on Shabbos. The Gemara is addressing the Melachah of Dash and the taking of Ma'asros on a weekday , saying that the same situation which will make one obligated in Ma'asros will make someone liable for transgressing Dash on Shabbos. If there is no Dash, there is no obligation of Ma'asros. We can understand from Tosfos the reason why there is no problem of Muktzah when there is no problem of Dash. This is why there is no question regarding the barley being Muktzah in our Gemara.
All the best,