How to present publication output on CV when you publish in fields where author ordering conventions vary?
I would suggest adding a remark like the following to your list of publications in your CV.
I publish in multiple fields, with different standards for ordering authors, some ordering by contribution and others ordering alphabetically. In the list below, first authors are indicated in bold when authors are ordered by contribution; the symbol = indicates a paper with alphabetically-ordered authors.
[1] Bozo T. Clown and K. N. Zhao. This is a chemistry paper. Science, 2014.
=[2] Bozo T. Clown and K. N. Zhao. This is a mathematics paper. Annals of Mathematics, 2016.
[3] K. N. Zhao and 4278 others. Higgs bosons are made of cheese. Nature 2020.
If this is for a job search/promotion: one way around it is to find yourself a champion to explain the situation for you, and leave it out of the CV. Your champion could be a (senior) collaborator who is writing a recommendation letter for you, or in the case of a tenure promotion, your department chair.
You can ask them to include a line when describing your most significant works explaining the conventions, something like:
In article [3] which I worked on together with Dr Zhou, he made the important contribution .... (footnote: conventionally the journal in which the research was published list authors alphabetically and not by contribution).
If it is not for a job search/promotion: I don't see why random reader of you CV would care.
Incidentally: I am quite surprised to hear the particle phenomenology orders by contribution; it is close enough to theoretical HEP that I would've thought the opposite (most articles on arXiv/hep-ph are listed alphabetically).
The concern here is that someone reading your CV may think that you have never had the lead role in a research project that led to publication. This is something that should be addressed in your recommendation letters. Your recommenders can say
"Dr. X spearheaded project Y and made the most significant contributions; of course she is listed as last author because in field Z we always order authors alphabetically."
It doesn't sound tacky coming from the recommender, whereas (as you correctly believe) it would coming from you. You should speak with your recommender(s) in field Z and make sure they raise this point in their letters. They can also make comments regarding your independence and leadership as a researcher in general.
You can also address this indirectly in your research statement, by referring to some of the papers where you are last author and describing the magnitude of your contributions to them.