I'm not an authority but anyway here is my answer. Firstly I want to point out that the occurrence of the collocation "except for" actually splits into two cases.
In one case it is a single lexical unit that is a preposition, hence accepting only noun phrases or equivalents as its 'object':
Everyone knew he was a fool except for himself.
The greedy want everything except for what they need.
In the other case the "for" actually belongs to a prepositional phrase, and it follows the usage of "except" such as in:
It offers a similar buffer option, except for books instead of video.
Here it parses as "similar except { for { { books } instead of { video } } }". Here "except for books instead of video" adverbially modifies "similar". Likewise:
He was blameless except in this matter. (takes an adverbial phrase and modifies "blameless")
He never takes advice except from Mother. (takes an adverbial phrase and modifies "takes advice")
The museum is always open except on Mondays. (takes an adverbial phrase and modifies "always open")
She ate everything except the meat. (takes a noun phrase and modifies "everything")
They will do nothing except sit here. (takes a verb phrase and modifies "do nothing")
I did not come except to help. (takes an infinitive and modifies "come")
The type of phrase Y that can be modified by an "except X" phrase has to be of the same type as X, except when X is an adverbial phrase and Y can be modified by X directly. Here are more actual examples with the "except" clause fronted:
Except among ideologues, there’s no ideal solution to these problems, and every remedy carries trade-offs. (Washington Post (2014))
Except among homesick Israeli immigrants and some Orthodox Jews who see living in the land of Israel as a religious imperative, there are precious few American Jews who ... (NY Times (2014))
Except among students of the modern papacy, Pius XI (Achille Ratti) remains an obscure figure. (Washington Post (2013))
Except under unusual circumstances, you should use the grammar and vocabulary of standard written English for these purposes. (NY Times (2012))
Except under khamsin conditions, nights in the desert are rarely very hot and may feel pleasantly fresh after the dry heat of the day. (BBC (2012))
Except when patients have been given blood or proteins intravenously, a rapid increase in total plasma protein concentration is always due to a decrease in the volume of distribution, basically to dehydration. (Journal for Respiratory Care & Sleep Medicine (2009))
Except possibly where a locally important species is very sensitive, freshwater aquatic life and their uses should not be affected unacceptably ... (US EPA (2004))
Except possibly under unusual circumstances not present here, we would not find a single conviction for a misdemeanor offense to be ... (US Justice (1988))
Except as provided below, no part of a White Paper may be reproduced in any material form ... (BBC)
Except with the prior approval of the court, the Secret Service shall not ... (US Code)
Except in the case of fraud, any action to recover penalties under this chapter shall be barred. (some US statute (2012))
Except on Israel, Unity Is Elusive At Islamic Summit (NY Times (1981))
Except these, there is no experimental indication for CP violation. (Physics Letters B (2004))
Except this there is nothing worthy of inspection. (The Description of Greece (1824))
There is also a specific usage with the subjunctive that seems less frequent now:
I will not go except you come with me. (normally it is "except if you ..." or "unless you ...")
Except one be born anew, he cannot see the kingdom of God. (ASV, Darby's, KJV)
Except a creature be part coward it is not a compliment to say it is brave. (Mark Twain)
I may have missed some details but I believe this kind of explanation is an adequate one for the major similarities and differences between "except" and "except for". For example it explains why we can say the first but not the second in each of the following examples:
I have not seen it except for when I was a child ("when I was a child" is a noun phrase)
*I have not seen it except for as a child ("as a child" is not a noun phrase)
You can take anything except this. ("this" is a noun phrase like "anything")
*You can take except this. ("this" is a noun phrase but there is none before "except")
So finally my answer to the original question is that both are valid English and mean exactly the same thing, although it might be better to delete redundancy:
Except [for] those built towards the end of his life, the buildings erected in Istanbul can be assumed to be his.
I grant that examples of sentence-initial "except" with noun phrases are rare, but since "except" with non-noun phrases aren't avoided at the beginning of proper sentences, I think the rarity for noun phrases is perhaps due to the fact that sentence-initial "except" is frequently used to join whole sentences. If that is so, then it may be that "except for" is used for noun phrases simply because it makes it easier to process. I myself would probably have chosen to use "except for", but I did not find the other one odd.