Fundamentally, there are 2 different questions here:
1) How can Seder Olam and modern Scholarship be reconciled
2) What does the Passuk in Daniel refer to.
The first question is the subject of an age old debate, often referred to as the question of the "missing 168 years." Scholars from Rav Saadiah Gaon until the modern Era have debated this. This question has already been dealt with on this site. However, the second part of your question, namely how to incorporate the verses in Daniel, has not as of yet been addressed, which is why I am writing this answer.
Since the issue of Seder Olam has been addressed, I will only discuss the second issue, and refer you to here for the first:
What is the explanation for the discrepancy between Seder Olam's chronology and that of historical scholarship?
Suffice to say, every approach either accepts Seder Olam's chronology and reconciles it with modern scholarship, or vice-versa. Obviously, if one chooses to accept Seder Olam, the Pasuk in Daniel is self explanatory, as the Rashi you quoted indicates.
However, if one accepts the chronology of modern scholarship (as I am inclined to do), the Pasuk in Daniel requires explanation. Ostensibly, Daniel is a contemporary to the Persian period, and it is far less feasible for him to be in error than it is for Seder Olam to be in error, written hundreds of years after the Persian Period. This issue is less commonly dealt with. The approach I am most familiar with is:
Daniel is listing only kings who had a significant influence on Jewry