In my experience, waiters will offer complimentary things differently than non-complimentary things. For example:
Can I get you started with something to drink?
This requires further feedback from you, which will usually involve reviewing the drink menu or knowing what you want (and thus understanding it costs something).
Would you like some chips and salsa to start off?
This is a yes or no question, which suggests it's being offered to you rather than suggested.
This isn't to say that a waiter couldn't say :
How about we get you started with some of our world famous jalapeno cheddar poppers?
Which aren't free, but in such cases, there is an implicit understanding that the customer will know it's not complimentary. Not because the customer is expected to know, but because if it was too ambiguous, enough people would say yes and upon discovering at the end of the meal that the item wasn't free would be some level of angry or upset, which would translate into complaints or bad reviews or lower tips, which would translate to that waiter not suggesting menu appetizers as though they might be complimentary.
In the US, it's generally safe to assume that water is free, and some item that is cuisine appropriate for the restaurant (chips at a Mexican restaurant, bread at an Italian restaurant, etc). So much so that they often don't ask. So some amount of experience can lead your understanding of whether an item is likely complimentary. If you're in a steakhouse and they ask if you'd like to start with some fried cheese sticks, and you've never had that offered to you at any other steakhouse, odds are good it isn't complimentary.
In any culture, I would assume that something is either usually complimentary or it usually isn't. Based on those cultural norms, you shouldn't be afraid to assume something is complimentary if it usually is. On the other hand, if you live in a culture where it is completely arbitrary whether one restaurant offers something as complimentary and other one doesn't, so that it is never safe to assume (which would be a bit ridiculous, but hey, I don't want to judge anyone's culture), then there is almost certainly a culturally-acceptable way of asking whether the offered item is complimentary or not. If the custom in that culture is to say "will that be free?" then you shouldn't worry about seeming stingy, since it is the agreed-upon way of asking. If the custom is to say "how much will that be?" then that's the best way to go. Point being, anyone's first line of defense in such a situation is to rely on previous experience, rather than panic about coming across as stingy or greedy or inconsiderate. Rather than asking "how to ask without looking stingy", perhaps the question should be: "how do most people in xyz culture handle this situation?" Try to learn the customs, rather than imagining a perceived slight.
Per your "house-made garlic bread and taro chips" situation, that sounds like weird customer service. I wouldn't expect it to be free either, and wouldn't hesitate to ask "oh is that free?" since bread is often free but fancy bread might not be. He should have said "would you like some of our complimentary fancy ass garlic bread" so as to avoid that ambiguity.
Furthermore, the fact that they ran out 20 minutes later makes it sound nonstandard. Who offers free things but doesn't make enough for all the customers? If it is some special perk they offer to customers lucky enough to come in when it is on hand, it should definitely be emphasized that it's complimentary.
And as for your colleagues being disappointed, that sucks. But people get disappointed all the time, so it's almost unavoidable that you will eventually disappoint someone for silly reasons, even if you try to do everything just right. Also, they might have just been disappointed that they didn't get bread, not that you didn't ask for it.
Asking if it's on the menu is clever, but if your default is to say no because you're worried it might not be complimentary, I suggest relaxing that instinct a bit and assume 90% of the time a waiter offers something specific at the start of the service, it's complimentary. Asking "I don't see water on the menu" every time is going to get exhausting and will seem a bit strange to many waiters.