Subtract time difference between two columns in a table
If you are only looking for the difference between two rows, you can reference them by their ids.

SELECT
  TIMESTAMPDIFF(MICROSECOND, s1.date, s2.date) DIV 1000
FROM 
  via1 s1
  , via1 s2 
WHERE 
  s1.id = 1
  AND
  s2.id = 2
;


There are a few errors in your CREATE TABLE statement:

CREATE TABLE via1 (
  id int auto_increment primary key, 
  sensor varchar(10) NOT NULL, 
  date timestamp(6) default current_timestamp(6)
);


You're using an old version of MySQL (5.5.44).  From the docs: 

11.3.6 Fractional Seconds in Time Values - MySQL 5.6 Reference Manual


  Before MySQL 5.6.4, the instances are limited in which a fractional seconds part is permitted in temporal values. ...when MySQL stores a value into a column of any temporal data type, it discards any fractional part and does not store it.