A Czech language developed from the Old Bohemian and the Czechs were always numerically superior population group within Bohemia and Moravia which prevented their assimilation. They made the majority of the population, and the systematic Germanization lasted only a few generations between the reign of Emperor Joseph II and 1848 to have the lasting and permanent effect of erasing the language.

The Czech culture, education, economic policies, social system was deeply influenced by German culture, and it was not always antagonistic. This is an interpretation of the 19th century national revivalists. While the Kingdom of Bohemia was a part of the HRE, it was really an independent entity with its own dynasty, Estate General, aristocracy, laws, church structure, and from 1424 even own religions following the teaching of Huss. The German influx into mining areas around 1300 waned during the reign of Charles IV (+1378) as the Black Death prevented wider migration into Bohemia proper from the Empire. The number of Germans within Bohemia is estimated to be around 15% at that time.

The main reason why Czechs were not assimilated in medieval times, is the Hussite Revolution (1419-1434/36) accompanied by long-lasting wars where the country was run as a military dictatorship by various parties opposing the Roman Catholic Church and the Emperor. The victorious Hussite party uprooted the Catholic church, which caused the bond between the Empire and Bohemia to weaken. Czechs /Bohemia cased to participate within the Imperial affairs for ~120 years. The Hussite Revolution was also ethnic upheaval, where Germans were targeted as pro-papal forces within Bohemia and Moravia. The German language islands were removed within Bohemia, but survived in Moravia (Jihlava, Brno, Svitavy).

The Estate General in 1424 started to push for Czech language as the only universal language of the communication within the administration, Hussite church, and the judicial system. The Czech language became the official language of Bohemia in 1500 under Vladislav II. The German language increased significantly in the middle of the 17th century following the 30-Years War in northern Moravia, western Bohemia, and northwestern Bohemia. The counter-reformation also supported the German language as the primary language of the Catholic church administration, and later time the Catholic Church was identified in the 19th century as an oppressor.

The German language was added as a second official language in 1628, but both languages coexisted until the reign of Joseph II as an official language of the kingdom. The administrative and bureaucratic centralization under Joseph II had an actually opposite effect, as the bilingual Czech-German Bohemia became on the surface officially German. This triggered the National Awakening phase, which was closed in 1848.

When it comes to your question of the topography played a role in the identity forming, it did certainly, but that was not really that important because the German speaking population lived in the mountain ranges. Bohemian and Moravian ranges were settled in the late Middle Ages while the valleys were settled by Slavs since the movement of the nation. Saxon-Bohemian relationships were generally good and can be traced to the 10th century. The main saint of Bohemia -St. Vitus- is shared by both Saxony and Bohemia. During the upheaval in one area, the refugees were flocking to the respective region. Saxons Catholics got asylum in Bohemia and Bohemian Protestants in Saxony. In the 19th century, the volume of goods traded between Saxony and Bohemia was far bigger than between Bohemia and the rest of Austria. The river port of Usti nad Labem/Aussig was the biggest in the Austrian monarchy, trading more goods than the port city of Trieste. The business and economic ties between these two regions did not have an effect on Germanization on Bohemia as Saxony was a different state entity.

The borders between Bohemia/Moravia and other non-Bohemian crown lands (Bavaria, Hungary, Saxony) were guarded since the Middle Ages. The border patrol was called Chods (The Walkers), while in Moravia, they were called Portas (from Latin Porta). They guarded the borders from unwanted visitors, smugglers, and invaders. Geographical barriers were sufficient in the forming the regional and later language identity, but only in a certain degree, because the lack of natural barriers in southern Moravia prevented assimilation in that region.