If you are using the REF= option on the CLASS statement in HPGENSELECT then it will automatically choose reference coding. This is a full rank parameterization and only those levels associated with non-reference levels will appear in the Parameter Estimates table.
If you remove the REF= option then HPGENSELECT will use GLM coding, which is the same as GENMOD uses. You will notice that just like in GENMOD, HPGENSELECT will set the reference level to 0 and have those levels appear in the Parameter Estimates table.
Either way however, the results from the two procedures will correspond to the same model fit and thus Log-likelihood values, predicted values, etc. will all the same. The differences will only be in the Parameter Estimates table and that is simply because of the different parameterization.
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