Just looked at all the pictures available from 01 to 05. 16 inch is the largest OEM rim and none of them have flush center caps. Some are more raised than others but none are flush.
Here is a list of every OEM rim for all versions of the Explorer in 2003. You will see a 17inch mentioned but only on the Explorer (4 door version).
2 Dr (Sport), (16x7), alum, 5 angular spokes
4 Dr, Sport Trac, (16x7), alum, 5 angular spokes
2 Dr (Sport), (16x7), alum, 5 straight spokes
4 Dr, exc. Sport Trac; 16x7, alum, 5 double spokes, w/openings in spokes, sparkle silver finish
4 Dr, exc. Sport Trac; 16x6-1/2 (steel)
4 Dr, exc. Sport Trac; 16x7, steel, 5 spokes, chrome
4 Dr, exc. Sport Trac; 16x7, steel, 5 spokes, painted
4 Dr, exc. Sport Trac; 16x7, alum, 5 double spokes, w/o openings in spokes
4 Dr, exc. Sport Trac; 16x7, steel, 8 spokes (chrome)
4 Dr, exc. Sport Trac; 17x7-1/2, 5 spokes (alum), satin nickle finish
4 Dr, exc. Sport Trac; 17x7-1/2, 5 spokes (alum), sparkle silver finish
2 Dr (Sport), (16x7), steel, 18 holes
4 Dr, Sport Trac, (16x7), steel, 18 holes
4 Dr, Sport Trac, (16x7), alum, 5 straight spokes
4 Dr, exc. Sport Trac; 16x7, alum, 5 double spokes, w/openings in spokes, satin nickel finish
4 Dr, exc. Sport Trac; 16x7, alum, 5 split spokes
2 Dr (Sport), (16x7), steel, 3 spokes
4 Dr, Sport Trac, (16x7), steel, 3 spokes
4 Dr, exc. Sport Trac; 17x7-1/2, 5 spokes (alum), chromed (Limited)
How about a picture???