I think I've found the answer (but I'm not 100% sure). I had to change this:

chainTxData = ChainTxData{
        // Data as of block 0000000000000000002d6cca6761c99b3c2e936f9a0e304b7c7651a993f461de (height 506081).
        // 1521311547, // * UNIX timestamp of last known number of transactions
        // 0,  // * total number of transactions between genesis and that timestamp
        //             //   (the tx=... number in the SetBestChain debug.log lines)
        // 3.5         // * estimated number of transactions per second after that timestamp
    };

To this in chainparams.cpp:

    chainTxData = ChainTxData{
        0,
        0,
        0
    };

That seem to have solved the issue and now I see "Progress 100%". It's the only thing that changed, the other things "Progress increase per hour", "Number of blocks left", "3 days behind" are still the same but the progress seems to have changed after I modified that section of the code.

UPDATE: When trying to use cpuminer-multi to mine, I receive this message:

JSON protocol response:
{
   "error": {
      "code": -10,
      "message": "Bitcoin is downloading blocks..."
   },
   "result": null,
   "id": 0
}

So it looks I was wrong and even if it says 100% it didn't finish the sync. It's because the chain has zero blocks? It doesn't count the genesis block for some reason?