Side effects are different for everyone. I find Flagyl unpleasant to take, but I don’t get lasting problems from it. It does come in capsules, but they’re a different dose (375 mg), which is more than I need.
I take VSL with breakfast and dinner, and my antibiotics at bedtime. I experimented and found that the antibiotics worked fine for me with once-a-day dosing. Sure the VSL would be more potent without antibiotics, but that’s not an option for me. My observation suggests that it’s still beneficial, at least at high doses.