Here is review415271003 for the 6.0 branch.

Here is review419361003 which ensures all tax rule applications result in unique taxes.

I think both reviews must be backported as it may result in wrong tax computation.

Here is review435351003 that ensures the same behavior in proteus.
But indeed it is not enough (even with issue10841) because as msg73970 shows it can happen when calling the on_change methods inside the ORM. Even if I do not think there is a valid case where tax rules should result in changing multiple taxes into the same tax, we should prevent the code to fail because of the unique constraint.

With issue10841 there is no need to make target_ids unique and it will anyway not solve the problem as only a unique constraint has the transactional ability to do it.
Any way proteus should behave like the other clients.

I guess your are not using 6.2 series as this should raise and error message since issue10841

For me the problem is that the ORM create multiple record of the same target in Many2Many when there is code to prevent that. Indeed I think it is because target_ids should be made unique.
Also proteus should behave like the other client and keep only unique instance of record in Many2Many.

At the moment I published review395481002 related to invoices. Missing sales, etc...

Scenario:

1. Create taxes: Tax1 and Tax2
2. Create a product: Product1 Add Tax1 and Tax2 in account category
3. Create a account tax rule: "Rule1". Add a new line:
   3.1. origin_tax: None
   3.2. tax: Tax1
4. Create a party: Party1. Add customer_tax_rule related to "Rule1"
5. Create an invoice: party is Party1 and create a new product: product1

When do on_change_product, len(taxes) == 3 but client only show two taxes: tax1 and tax2

Now, open a trytond-console, and do same operation.

>>> transaction.set_user(1)
>>> User = pool.get('res.user')
>>> context = User.get_preferences(context_only=True)
>>> transaction.set_context(context)
>>> Invoice = pool.get('account.invoice')
>>> invoice = Invoice(1)
>>> InvoiceLine = pool.get('account.invoice.line')
>>> Product = pool.get('product.product')
>>> product = Product(1)
>>> invoice_line = InvoiceLine()
>>> invoice_line.invoice = invoice
>>> invoice_line.product = product
>>> invoice_line.on_change_product()
> /home/raimon/projectes/nandev/049296/trytond/trytond/modules/account_invoice/invoice.py(2197)on_change_product()
-> self.taxes = taxes
(Pdb) taxes
[1, 30, 30]
(Pdb) c
Pool().get('account.invoice.line')(**{'taxes': [1, 30, 30], 'unit': 1, 'party': None, 'unit_digits': 0, 'company': 1, 'product': 1, 'invoice_type': None, 'account': 1588, 'invoice': 1})
>>> from decimal import Decimal
>>> invoice_line.quantity = Decimal(1)
>>> invoice_line.unit_price = Decimal(1)
>>> invoice_line.save()
>>> invoice_line.taxes
(Pool().get('account.tax')(1), Pool().get('account.tax')(30), Pool().get('account.tax')(30))
>>> Invoice.update_taxes([invoice])
>>> invoice.taxes
(Pool().get('account.invoice.tax')(1), Pool().get('account.invoice.tax')(2))
>>> invoice.untaxed_amount
Decimal('1.00')
>>> [t.base for t in invoice.taxes]
[Decimal('1.00'), Decimal('2.00')]
>>> [(t.tax, t.base) for t in invoice.taxes]
[(Pool().get('account.tax')(1), Decimal('1.00')), (Pool().get('account.tax')(30), Decimal('2.00'))]

SQL:

# select id, line, tax from account_invoice_line_account_tax;
 id | line | tax 
----+------+-----
  7 |    3 |   1
  8 |    3 |  30
  9 |    3 |  30

Bug:
- Invoice line has three taxes: tax1, tax2 and tax2
- update_taxes(), the base from tax1 is 2.00 and not 1.00 (from total taxes in invoice line)

Reason:
New tax_ids are added in current list (extend). We need to set() unique taxes.

https://github.com/tryton/account_invoice/blob/6cb358db41d9c300934d8cfffa15bd04354509be/invoice.py#L2260