Convert to julianday, which is floating point, correct the offset (origin date) and then correct the slope (unit scale) ...
select (strftime('%J', '2016-06-13T09:36:34.123Z') - 2440587.5) * 86400.0;
1465810594.123
or
select (julianday('2016-06-13T09:36:34.123Z') - 2440587.5) * 86400.0;
1465810594.123
The number 2440587.5 is the epoch adjustment to the unix epoch date:
sqlite> select julianday('1970-01-01 00:00:00.000Z');
2440587.5