I think enough people have confirmed the same in this thread. As far as conversion of a license into a Swiss one is concerned, it does not matter if you take the test on a manual or automatic.
I didn't see first that your license was a conversion so I can't say for sure with that though.
What I can say though with 110% certainty is that for a persons first test if they pass with an automatic transmission then they can only drive an automatic. If they pass with a manual transmission they can drive both.
Brian.
On the other hand, it does not really matter as long as you can drive and do it safely.
Ok this was about 12 years ago, but in the case of a conversion, they take your old DL, and depending on the format of the issuing country/state, the specification of an automatic/manual may not be there. If there is no specification of 'automatic only', the Swiss issue an unrestricted Swiss license. (even if you only ever drove an automatic)
For example, in US, the majority of liscenses don't specify even though probably near 100% took test on automatic.
In recent years, Swiss have changed law, not sure for all foreign liscenses or only non-EU, but in addition to just paperwork conversion, they make you do practical test, but as I understand this is not the same a getting a liscense, just to confirm you are a decent driver.
I always consider myself fortunate that my dad insisted I drive his manual when I was learning to drive in the US. If I went out in my mother's automatic station wagon, I then had to go out the next time in his little manual. I never used those skills much whilst in the US, but once I moved here I was grateful that my father did that. Even 20 years later, I could still hear him yelling at me to get my "damned foot off the clutch!"