The evidence sure seems to point to a later modification, I agree. Especially if the stove is indeed pretty generic, and on a cement slab. Having started my railroad career in Durango with the D&RGW, and then transfering to Salt Lake after the sale to Bradshaw, I have seen a few stove installations, but never one on concrete. I do seem to recall seeing a couple on sort of a sandstone looking stuff, framed by a steel barrier, but, my experience has been that they usually used asbestos panels...usually covered with tin for both the backwall..and the floor. Two stove designs were pretty prevalant...the caboose stove, and a larger, more generic "house looking" stove. This could be the one you seen. Don't know. I assume you found the numer 3611 on the inside...is a bit suspicious, as well, that it did not include a 0, or an AX.
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The doorway puzzles me a bit tho....if it was cut out after the car was placed on the ground, as a doorway, Why not remove the pin lifter, and cut it all the way to the floor level? Seems odd. And...as I mentioned before, the work on the modifications, does resemble a lot of the Grandes work on other cars.
What we all sometimes forget is that the Rio Grande was in the business of getting equipment back out on the road working...and the lack of a stencel, or time to use it..or proper color of paint, or maybe even getting time to let someone know in the records dept that the equipment was modified, was very often overlooked, rather than hold the equipment in the shop.
Another idea you may find a bit hard to believe, but true, a B&B gang, or water service man, may have modified the car assigned to him, without authority...I've seen it done here in Salt Lake...and gone out of his way to make sure that it was never "noticed" in the official rosters, and such..
All speculation, of course, But my 2 cents worth
Doug