Traveling with 18 month old to Vienna, Switzerland, and....

Not all rental cars can cross borders, and many countries have required vignettes one needs to purchase. Also, the daily fees on car seats are quite expensive. Trains are probably the most efficient mode of travel , and would allow your toddler to move about.
How many nights do you actually have in country- 11?
Vienna is a great city to explore- I think you have too much on your wish list.
Perhaps narrow down your list for the five nights after the conference - three countries in five days doesn't really work.
And - my "must- see" could be a snooze for you. What are your interests, that align with a toddler?
I'd encourage you to firm up your itinerary soon, as May is a busy travel month- shoulder seasons- and family lodging- are disappearing quickly.
Wishing you a wonderful family trip. Safe travels.

What do you want to see? Possibly German, Italy, and Switzerland, plus Slovakia and Hungary will most likely take more time than you have.

Be aware that Zurich is 8+ hours by train from Vienna. If you have from the 19th to the 23rd post-conference, I suggest you spend two nights in Salzburg and three in Switzerland. You could daytrip to Melk or to Slovikia on one of your conference days, but that's about it. BTW, I could spend the entire trip in Vienna and not be disappointed.

I was thinking we may get a car or do a day tour one day to Slovakia
and Hungary while in Vienna.

A day tour? I guess I'm a day you could do some justice to Bratislava and Gyor, or maybe Sopron. But a long day.

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You seem to forget that you are traveling with a toddler.

After your conference stay two days more in Vienna, then go to Salzburg for three days. Eventually go to Zurich for flying home.

You only have 6 days. Pick your dream location and go spend the time there.