I think Hacham Ovadia has a footnote in Hazon Ovadia on Pesach (and probably elsewhere) in which he discusses why we don't use the pausal form of gafen instead of gefen. He writes (if i remember correctly) that "amen" is really the end of the statement and not gefen. Shouldn't the same apply to the beracha in Bircot HashShachar where we say "shelo asani aved"? Shouldn't it be "eved"? All the siddurim I've seen have "aved". If you hear someone say each beracha are you not supposed to amen? plus, neither is really DEPENDENT on other people more than the other one?
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Your answer is in your question. "Shelo Asani Aved" does not really have "amen" included as part of the bracha. The bracha is meant to be said to yourself, and you are not supposed to be saying it for others. (which would assume an "amen" as part of the bracha)
To lay this out more clearly.
For wine said over kiddush, the custom is for the leader to say the bracha, and for everyone else to have fulfilled the obligation of the bracha by them saying "Amen". The "Amen" is therefore intended to be part of the bracha.
For the morning blessings, originally, each person would say the brachot to themselves as they got ready during the morning. Depending on the shul you go to, you might have a person saying all the brachot and people responding Amen, or the congregation may not say the brachot communually at all. Thefore, "amen" can not be part of the bracha, as it may or may not be responded to, even when other people are around to hear it.