Actually, by every metric, he is being overpaid by several million a year.
MANNY MACHADO'S CALCULATED MARKET VALUE
After applying our Prime % figures into our base calculated value, we're given two values. The average of these values becomes our current calculated market value.
TERMS AVG. SALARY 6 years, $160,692,246 or $26,782,041 per year
https://www.spotrac.com/mlb/san-diego-padres/manny-machado-11638/market-value/
The Padres had to overpay in order to get him to sign with them.