The question is about the location, not the makeup of the altar. Whether it was made of uncut stones is an important consideration, but not relevant to the question. Torah is clear that the only authorized location for sacrifices was at the Tabernacle altar, and the only people authorized to make a burnt offering were the sons of Aaron. The text implies that Manoah made the offering himself on a rock in his own field, yet God clearly approved.
I suspect there are one of two things going on.
- Manoah was ignorant of the specific commands regarding sacrifices and God honored his intention despite his imperfect execution.
- Manoah, his wife, and the angel all traveled to the tabernacle at Shiloh and engaged the assistance of the priest on duty, although none of this is stated in the text.
I prefer the first answer, since the second requires too many important details to have been left out of the story. If so, then the answer to the original question is YES, Manoah's sacrifice unquestionably violated the command against sacrificing "anywhere you please". Fortunately, ours is a compassionate and forgiving God who works with us where we are, even while he encourages us to keep moving to where he ultimately wants us to be.