The flight crew inside the FAF flying an RNAV (GPS) 4L approach to BTR using LNAV only guidance; descended below the MCA at an intermediate waypoint; HOGTO; and received an EGPWS obstacle warning. They initiated the mandated go-around but abandoned doing so when they entered VMC conditions and were able to land safely.

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The reporter provided significant additional information regarding both the aero chart format and the installed Collins FMS systems.He felt the commercially provided IAP profile view was insufficiently precise as to the meaning of the 820 FT printed below the phantom Glide Slope symbol between GOCET; the FAF; and HOGTO waypoints. This confusion had significant impact on the ultimate CFTT event. He was confused but; ultimately; felt it was a Glide Slope crossing altitude which was not applicable to the type of approach they would be flying which would not utilize a software provided glide path.Reporter was perturbed by the fact that; although HOGTO was included in the FMS database; it was not included in the Line Selectable GPS 4L approach. He had the First Officer install it manually; a practice he later learned was proscribed by company SOP.Of interest; although the installed FMS was capable of and did; in fact; produce a software developed Glide Slope; company SOP required that GPS approaches be flown as LNAV only approaches utilizing classic 'dive and drive'; non-precision approach techniques and compliance with the applicable MDA minimums; in this case 620 MSL rounded up to the nearest even 100 FT (700 MSL).Ultimately; when the flight was re-vectored due to separation issues and the approach reinstalled sans the manual insertion of HOGTO; the subsequent approach was flown precisely in accordance with company SOP. HOGTO was correctly NOT inserted and the approach flown in classic non-precision manner following company SOP. As a result; upon crossing the FAF (GOCET) the First Officer put the MDA (700 MSL) in the altitude window and a typical 1;000 FPM descent was initiated; the unplanned result; therefore; being that the 820 MSL crossing restriction at HOGTO was not complied with and the further descent towards obstacles; clearance from which the restriction was intended to provide; resulted in the EGPWS warning and the subsequent pull-up; ultimately canceled as they became VMC and landed safely.The reporter advised that; as a result of his safety report; the company has modified their SOP regarding GPS approaches and directed flight crews to 'NOT' accept clearances for approaches for which all published waypoints are not presented upon single button 'line selection'. In that regard he stated that his next destination; PHF; had just such an approach; the RNAV (GPS) Runway 20 wherein waypoint ROBOY is not included when line selected although; again; it is in the FMS database and could be manually inserted--although doing so is still precluded. He is uncertain how many other instances of this are in the airline's FMS databases.In summary; the reporter felt the commercial aero chart needed to be modified to make it clear the 820 FT altitude was; in fact; a crossing restriction at HOGTO; and that all waypoints that delimit procedural flight path constraints be included not just in the FMS database but in any and all line selectable approaches that utilize them.