Well it clearly depends on the capability of the tools, probably your question can be more likely be answered in a Mass-Spec forum or at the (Github) pages of the packages.
Are you looking for an universal solution or for something that matches your datasets?
Even when they used a certain method as showcase it doesn't mean it's not working with another one.
The LC shouldn't make a difference. In any case you should be able to identify the compounds with their retention time and m/z. However it could be possible, that some peak-integration defaults are hardcoded in the tool that simply do not work with all possible separation types. In a perfect world you can adjust this - as far as I know XCMS offers a lot of flexibility.
The MS however can make a difference, just because the data look different if you just have MS or MS/MS. In the latter case you have more dimensions, not every software might be designed to work with this.
Matthias