The gemara asyas that in the second beis hamikdash they expanded the mizbei'ach, either for practical reasons or because they wanted to incorporate a plumbing system for the wine pouring. The gemara asks how they were able to add to the dimensions of the mizbei'ach, based on the pasuk of הכל בכתב מיד השם עליה שכיל כל מלאכות התבנית, which basically means that all the areas of kedusha and their measurements were taught to Dovid and couldn't be changed. The gemara answers that the area that they sanctified to contain the mizbei'ach that was taught to Dovid was 60 amos. Rashi explains that Shlomo didn't understand the drasha from the pasuk and therefore made the mizbei'ach smaller, but the b'nei ha'gola in the time of the second beis hamikdash darshened it and added on to the size of the miz'beiach. The gemara then explains that many aspects of the mizbei'ach were essential but the length width and height weren't essential and were able to be expanded and contracted as deemed necessary. Therefore, even when they added to the mizbei'ach they didn't take advantage of the entire area to make it as large as possible, because it wasn't necessary for them (it isn't clear to me why rashi has to say that Shlomo wasn't able to darshen the pasuk and didn't know that it was expandable up to 60 amos - why not just say that Shlomo felt that although it could be expanded, he didn't need to make it any larger).
Rashi in chumash (parshas teruma) writes on the pasuk 25:8 - וכן תעשו that in the future when the beis hamikdash would be built they would have to make the vessels similar to those of the mishkan. The Ramban asks on rashi that in divre hayamim 4:1 when it describes the copper mizbeiach made by Shlomo, it says that it was 20 amos by 20 amos, which didn't resemble the one made by Moshe (which was either 5x5 according to the simple reading, or 10x10 according to R. Yehuda 59b)? The Maharal doesn't understand why the Ramban asks this question on Rashi as if Rashi was saying on his own that וכן תעשו is לדורות for the vessels of the Beis HaMikdash. Rashi is sourced in the gemara in shavuos 14b. To answer the Ramban's question the Maharal says that the requirement of וכן תעשו - לדורות is only on movable items, but the mizbeiach which was attached to the ground like the mikdash iteself wasn't bount to this rule. Just as the actual structure of the mikdash and courtyards were very different in dimensions form that of the mishkan, so was the mizbeiach. In truth, rashi never mentions the mizbeiach, only the shulchan, menorah, kiyor.... The Mizrachi answers that the requirement of וכן תעשו is not on the dimensions, rather on the shape and general form.