What is the difference between saute and caramelizing toppings?
Caramelising is a chemical process in which sugars decompose under the influence of heat (pyrolisis). It happens to any heated sugars, no matter if they are free (as in heating refined sugar for making candy) or bound in something else (such as the sugars naturally occurring in an onion). The outcome of the process are compounds which have a dark color and pleasant aroma. 

Sauteeing is a cooking technique. It consists of frying small pieces of solid food on very high temperature with very little fat while shaking the pan all the time, so they won't overheat and/or stick. 

Many people don't know the technical meaning of sauteeing and use the word for plain shallow frying at medium temperature and without shaking the pan. This seems to be the definition your employer was using. 

In fact, you were shallow frying both kinds of vegetables, which resulted in caramelisation plus other changes for the onions and in these other changes only for the vegetables which don't contain significant amounts of sugar. 

Cooking recipes frequently avoid saying just "fry the onions", because onions have to be brought to a different state for different recipes. So they usually use a word which implies a desired final state, such as "caramelize". For many other vegetables, which only have a single usable state of doneness, they specify the technique instead. This is why different words can be used for the same process - one describes the technique you are using, the other describes the changes which are happening, it is like saying 'I am going sunbathing' or 'I am going to catch some tan', which are indeed the same process. 

Incidentally, true sauteeing is a bad idea if you want to caramelise onions. Low and slow is the way to go if you want caramelised onions, while during the high temperatures used in sauteeing they go from translucent to burnt without passing a nice caramelized stage. But just leaving them in the pan for some time is a good technique. 

You also say grilling. This is a completely different technique, and it is done on a grill instead of in a pan. I can't imagine how you would caramelize cut onions on a grill, unless you put a griddle on the grill, which is equivalent to frying.