You are 3-4 months ahead of Ally moving to invoicing in Mexico and I would be interested in anything you learn in the process. We have a similar problem in Canada where there are multiple taxes. The work around we came up with was to have the sales tax assigned to a line item but to add the other taxes as new line items on the invoice. Less than ideal and I don't know what issues we will encounter when we start to eInvoice (not an issue in Mexico, can't do).
We have been doing manual invoices in Mexico a little over a year. This is the first time we have run into this issue. We haven't resolved this yet but up til now we haven't had any issues with invoices. We are using a slightly customized version of the P2P invoice tool to do our invoicing in all countries other than Canada.
As for Canada, we had a working solution for the multiple tax types on one line item in Ontario (the only province we are rolling out to currently). However, before we went live they changed the tax laws in Ontario. They are now using the Harmonized Tax, HST. This does away with that issue from my understanding. We are now in the process of reworking the tax codes for the new process and will be implementing in the next few months.
You are able to do multiple tax types on a line item. This works fine where you have GST and PST on a single line item. You are forced to do line item taxes in order to make this work.