This only matters if you actually have the chance to USE the DTT
If you stay <183 days in Cyprus and at the same time some other country claim you are tax resident in that country because of its domestic rules you are fucked big time because Cyprus will revoke your
tax residency.
You are right that the tax residence
certificate based on domestic law is quite worthless in protecting you against taxation in other jurisdictions.
However, if there is a conflict between the provisions of a DTT and domestic law, the provisions of the DTT will usually prevail.
The DTT primarily helps determine which country has the right to tax a particular source of income.
To access DTT you will need to inform the tax authorities of both jurisdictions. This is usually done through a formal process where you declare that you are a resident for tax purposes in one of the countries under the treaty, and you are claiming the treaty benefits.
Different countries have different procedures for claiming treaty benefits. You may need to fill out specific forms or provide additional documentation.
For example, In the U.S. non-resident aliens typically need to complete form W-8BEN to claim treaty benefits.
Estonia issues automatically tax residence certificates based on DTT-s, which you can then present to tax authorities in other jurisdictions.
Cyprus and Spain have their own forms and procedures.
Once you have filled out the appropriate forms, you need to submit them to the relevant tax authority. This might be as part of your annual
tax return, or it could be a separate process.
The second issue is the corporate tax. The mere fact that a company is incorporated in Cyprus and pays taxes in Cyprus on its worldwide income (and therefore able to obtain a Tax Residence
Certificate from the Cyprus Tax Authorities) is no longer sufficient for a business to guarantee that a
Cyprus company can access the full treaty benefits offered through the expanding and favourable DTT network that Cyprus has to offer. Most tax jurisdictions will now examine whether the Cyprus company claiming tax benefits has substance, and is not just a shell company set up merely for tax purposes.