After reading the code of MRP and Procurement modules, it seems that my question targets the wrong module.

The MO (Manufacturing Order) is generated from the OP (Procurement). And it is the OP that holds the quantity to be produced.

• Selling a make to stock product (or with sale.order.line's procurement method set to 'from stock') the MSR (Minimum Stock Rule) will be checked. If that MSR has qty_multiple set, then it will be used to round the quantity manufactured by that number. (lots of 10 products in my case).
• Make to Order products (or with sale.order.line's procurement method set to 'on order') the MSR is not used, leaving the Scheduler to create a MO for the exact quantity needed.

The BOM will only define how much of product(s) is required to produce such or such quantity.

Conclusion :

• I cannot tell the ERP to produce with quantity_multiples according to BOMs.
• I can only tell automatic procurement to replenish the stock with quantity_multiple option defined in MSR for one product. The same quantity_multiple applies whatever the BOM.

One more option I could explore would be to use multiple MSRs to define several quantity_multiple for different locations and playing with location chaining to land all product in the same location, but that sounds rather complex.