Hello,
You ask a lot.
I hope some other will help.
I think you can handle 80% of what you ask with Axelor.
Axelor is not perfect, full complete … and your situation implicate different structures, complex taxes …
But for all you ask, there are functionality, possible options … maybe you’ll want something not implement and your project can’t be success. But if you can develop it or find someone for do it, it will be the perfect solution.
- Company base in Malta => should be not a problem.
Two possibilities for test Axelor easier :
1 - https://demo.axelor.com/open-suite-fr/login.jsp
2 - use a docker-compose
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Bank accounts => should be not a problem.
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Merchant accounts (e.g. Paypal) => I don’t know what you expect and what it’s possible on Axelor for import data / send order …
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MT and GB VAT registrations (with plans for further VAT registrations in DE, FR, IT, ES, PL, CZ) => flexible configuration, so I guess it’s possible want you want
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VAT reports need to be in the currency of the relevant country (e.g. GB VAT = GBP) without currency moves (e.g. not converted to EUR base currency then converted back) => your configure is base on %, so whatever the currency value.
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Invoice sequences based on VAT registration (e.g. DE VAT would be DExxxxxx) => « invoice sequences » ? If you mean the VAT number of the society, it’s not a « sequence » like the word is use on Axelor. You can identify every society with the VAT number. And so for every society you have the VAT number you want (not only number but alphanumeric).
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Credit note/refund sequences to be based on VAT registration (e.g. FR VAT would be CNFRxxxx) => I don’t know what’s mean
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Correct VAT number based on VAT registration => if you ask if they are a request on legal society register. No Axelor don’t have it.
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Using warehouse in GB, but planning on expanding to warehouses in DE, FR, IT, ES, PL and CZ => about Storage place, you have a lot of possibilities (virtual storage, group/parent storage, physical storage …) you can plan deliveries between storage, make inventories, correction of stock …
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Automated VAT determination or sales (based on warehouse country, destination country and destination postal code) would be helpful but not essential as this can be carried out separately and imported via REST API => about API, I don’t handle it, I’m sure you will find all you want
(for the rest of the question read my advise below) -
Cross-border stock moves between countries are reported monthly so would need to self-invoice for the moves from one VAT registration to another, using reverse charge and EC sales list - happy to use REST API for this if necessary. => with a good organization it can be easy to do it.
My advise :
Axelor have a very good potential (I don’t work for them 
). I use Axelor for my society since January 2020.
It works for production, but it’s not perfect. I’m on last version and I have a bug for doing my invoice since 15 days…
For your situation, I think you can use Axelor.
Buy, stock, delivery, invoice, banks, currencies, VAT, API… have a lot of possibility for your business.
Learn to create headquarters, Subsidiary company, society, warehouse …
Skip over a French conversation will be appreciated