At least in the 14th Century, the Empire wasn't particularly fragmented by the standards of Western Europe. The Emperor retained a reasonable level of control (for the time) over the individual princes of the Empire, even if they did exert some (usually nominal) control over the election of the next Emperor, and other such functions, much as the vassals of a lot of the other feudal kings of the period had some degree of power and influence over their royalty. This is reflected in contemporary maps.

Much as in those countries, feudal relations that gave significant power to a fragmentary collection of lords controlling areas of land within the kingdom (or in this case, Empire) were a necessity for most countries due to the difficulty of organising a centralised authority; even communicating messages from a central point was extremely time-consuming, and was thus reserved in most part for issues of significance, meaning that the particularities of local government had to be dealt with locally too.

Maps like to display the territorialised nature of the Empire even in earlier years, however, for two primary reasons: first, that the princes of the Empire exerted much more consistent influence on the Empire than would be normal in other feudal countries, and second that it helps us understand what would otherwise seem to be the sudden territorial break-up of 1648 (after the Treaties of Westphalia and Münster) much better.

However, the exact development of the Holy Roman Empire's institutions, that formalised de jure the level of control the princes exerted over the Emperorship in a way that was merely de facto in many other states, meant that rights secured by the princes - such as the privileges of the Reichstag (Imperial Diet) or the organisation of the Kreise ("Imperial Circles", a sort of autonomous unit of government) - were harder to whittle away when material conditions developed in such a way that further centralisation became feasible in other countries.

Furthermore, when dynastic power struggles occurred in the Empire, the critical role of the princes of the Empire in giving legitimacy and power to their ruler of choice meant that appeasement was common. Quoting Wilson,

...high politics continued to make a social impact. The rivals for the German crown after 1250 granted immunities and privileges to lords and towns to win their support, while relative royal weakness provided more scope for initiatives in revising existing legal and social arrangements.

This was not uncommon to see when a dynasty lost control of the Imperial throne, and various authors (such as Wilson and Whaley) have argued that the concept of "German freedoms" were formative in German national identity, as something involiable and core to the common experience of German-ness.

This, combined with the level of religious fragmentation across the Empire after the Reformation (seen here), meant that the Thirty Years' War was concluded with a significant lessening of Imperial authority in favour of princely power(for reasons that I'd be happy to explain in a comment), and indeed maps of the period showed the Empire as broken up much as modern ones might, in a way that was not seen earlier. I hope this answers your question!

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Bibliography:

Koenigsberger & Mosse, Europe in the Sixteenth Century

Matthew, Atlas of Medieval Europe

Wilson, The Holy Roman Empire

Whaley, Germany and the Holy Roman Empire 1493-1806 [Parts 1 & 2]