The longer ones will protrude 1/8 inch more into the interior of the heater and that won't matter one bit (at least to me). If you are designing a heater from scratch, you may not want the longer screws picking up dust but for normal use it won't matter and you can't see into the interior once installed.

Kent

1937 Chevy 1/2 ton
1942 Chevy 1/2 ton
1947 Diamond T Model 509
1951 Chevy 1/2 ton
1950 Chevy COE Model 5700 ~ "Barney" ~ And more pix