The first item is that no one actually knows, with certainty, what Archduke Ferdinand's plans were for the structure of the Empire after he became Emperor-King.

We do know that he hated the Hungarians on a general level (we can not prove he hated all Hungarians individually). In the English language work centering on the Archduke The Assassination of the Archduke: Sarajevo 1914 by King and Woolmans he is quoted as saying

"The so called decent Hungarian simply doesn't exist and every Hungarian, be he a minister, a prince, a cardinal, a tradesman, a peasant, a stable boy or a servant is a revolutionary and an ass."

There is also a general opinion that Ferdinand would have wanted to do SOMETHING to change the dynamic of political power. What that specific plan is, he never definitively said. Possibly he would want to create a "Tripartite" state, with Austrian, Hungarian, and Slavic political bodies. King and Woolmans say that this was his first conceptual plan.

Christopher Clark, in Sleepwalkers offers the observation "By 1914, however, it appears he had dropped this plan [the tripartite state plan] in favour of a far-reaching transformation by which the empire would become a 'United States of Great Austria,' comprising fifteen member states, many of which would have Slav majorities." This statement would reflect the concept of the "United States of Greater Austria" promoted by Hungarian Romanian Aurel Popovici in his 1906 work Die Vereinigten Staaten von Gross-Osterreich (available for free on google books, but in German). Further, the Archduke did meet with Popovici in 1909 on a trip to Bucharest and was certainly aware of the Romanian's work.

King and Woolmans assert that by 1912 the Archduke, inspired by a visit the the United States of America, had taken to the federated states plan. Here the authors are relying on the personal memories of both Ottokar Czernin (a friend of the Archduke and later Foreign Minister for Austria-Hungary) and Albert von Margutti (A military aide on the staff of Emperor Franz Joseph). They note:

When Margutti pointed out how difficult a legislative transforming of the Dual Monarchy into the Empire of Federated States would likely be, Franz Ferdinand insisted that it could be done "by force."

We can never know to what extent that comment was sincere intent or blustering bravado made in private correspondence. The violent realignment of internal Imperial politics would have been a very complex and potentially very expensive project in terms of political capital, economic loss, and actual monetary costs.

I wanted to establish all that because part of the issue is we don't have any official maps for the proposal, nor any commentary from the Archduke describing what his map would look like. So even if we are willing to assume that the Archduke was committed to a Federated Empire, why isn't Bosnia on the map? Obviously, he would have had to address Bosnia in some way!

Since there were never any official proposal maps introduced, the map that is generally used is the one Popovici made in 1906. In 1906, Bosnia was NOT part of Austria-Hungary, and it is therefore reasonable that Popovici did not include it on his map. It also would have been reasonable if he HAD included Bosnia, because by that time Austria-Hungary had occupied the region for 28 years, but strictly speaking Popvici was correct to not include the territory.

Austria was given the right to occupy Bosnia in the 1878 Treaty of Berlin, but De Jure this territory was still part of the Ottoman Empire. Austria made some small efforts to play along with the fiction that they would ever return Bosnia to the Ottomans. They changed the legal code gradually, perhaps too gradually in the opinion of Peter Sugar, expressed in Industrialization of Bosnia-Hercegovina, 1878-1918, and they respected local traditions as best they could. However, they also integrated Bosnia into their customs union, they recruited soldiers from the local populace, they appointed governors, and they invested large amounts of money into economic projects and infrastructure such as roads and railroads. However, even after 30 years of integration and investment, the technical truth remained that Bosnia was Ottoman land until the 1908 annexation and all the diplomatic wrangling that was required to turn "De facto" into "De jure."

So we don't know what his plans would have been, and Bosnia isn't on Popovici's map because it wasn't legally part of the Empire and Popovici was being rigorously accurate.