Your Coworkers' Perception
You mention that your coworkers might be seeing you as taking too many breaks, but it might also be purely your own self-consciousness. So, I would start there. Some questions to ask yourself to see if it's an issue:
- Do you have any evidence that people are paying attention to your breaks? For example, have you gotten comments or dirty looks?
- Are your breaks really that different from everyone else's in length or number?
- Are you the only person who regularly snacks at work?
For some context, I worked at one office where two 15-minute breaks a day for coffee, chitchat, and maybe a snack were customary. In other places, taking a break that long that wasn't part of your unpaid lunch would be seen as slacking. Likewise, some office cultures are big on food, with people bringing in food to share, or keeping snacks at their desk, while others not so much.
You mention eating at your desk annoying your colleagues. Again, is this something they've said to you, or just an impression you get? I would avoid this if you know it's bothering or distracting people, especially since you'd rather not anyway.
If you find that you do have a perception problem, then you can do some things to address it. The specifics will depend a lot on your office, your diet, and even your status as salaried or hourly.
If you're paid by the hour, then making sure to keep accurate track of any breaks and working extra as needed is important. If you're salaried, it's less so, but you don't necessarily want to be seen getting in at the same time as everyone else, leaving the same time as everyone else, and taking more breaks. By the same token, getting into the office early and/or staying late tends to make people view you as more productive. (It's not necessarily accurate but we're talking about perception.)
As much as you can, try to minimize the effect of your breaks on your coworkers. For example, if Bob usually comes by to ask about the status of XYZ around ten, that might not be the best time for a mini-meal break. Likewise, if all the smokers congregate outside at 9:30, that's probably a great time to go get something to eat.
You can also, as much as your dietary needs allow, pick things that are quick to eat. For example, a shake or smoothie would be quicker than a sit-down meal, and might be something you could have while working or on the way to or from work. I don't know if that's feasible for your specific diet, of course.
Aside from that, anything you can do to be a good coworker will improve your overall perception, which makes people less likely to obsessively track your break time. You want to be known as friendly, helpful, and on top of things, and you don't want to be the guy who leaves a mess in the microwave, or complains about everything, or blows off requests for assistance.
Your Boss's Approval
You mentioned that this is usually only a problem for bosses who don't approve of your eating habits, or, to put it more bluntly, have some stereotypical ideas about how people are "supposed to" eat that are probably related to culture, class, masculinity, and a bunch of other stuff that's outside the scope of a Workplace SE discussion.
In those situations, your best bet is probably to keep any explanation brief and try not to make a big deal out of it. Depending on what activities you're doing outside of work, mentioning them specifically might actually score you points, or it might be viewed as a negative. (I get the impression that those bosses would probably think it was cool if you were, say, training for an Ironman marathon.) So, use your best judgment to determine how much you want to mention.