Air carrier Captain reported there is a lack of officially published information regarding an aligned taxiway at GJT.

Narrative

Prior to the occurrence at the gate; an appropriate briefing took place which also took into account a review of the 10-7 pages and airport NOTAMs. There was nothing remarkable about the taxi out or takeoff from Runway 11 noted on the 10-7 nor any NOTAMs alluding to anything unusual for Runway 11. A quick glance at the airport diagram showed what would look like an uneventful taxi to Runway 11. No further briefing was done as it relates to any special taxi or takeoff roll considerations for Runway 11 based on a quick glance at the Airport Moving Map (AMM) chart; and thoroughly reviewing the 10-7 pages. The taxi out and takeoff occurred just prior to the sun coming up over the mountains; but with adequate daylight available. The airport surface lights were not on during taxi and takeoff.As we began taxiing out to Runway 11 via Taxiway Alpha; I took my time as we waited for our 5-minute engine warm up time. As we moved towards the end of the runway; I saw on the AMM chart that Taxiway Alpha continued past Taxiway A2. However; Taxiway A1 was just greyed out on the AMM chart. I then saw A2 went onto the runway; and the threshold was a bit further down. At a glance I made an assumption that there was a displaced threshold at play; and that A2 was just the new beginning point for Runway 11. I asked the First Officer (FO) if he saw what I saw on the diagram that A2 was the beginning even though Taxiway Alpha showed pavement beyond A2 on the AMM. At that point; the FO pointed out ahead of us that there were in fact taxiway lights blocking the path on Taxiway Alpha beyond A2.As we got to Taxiway A2 we had the appropriate runway hold short markings; and a sign that read Runway 11 along with Runway 11 notated on the pavement. As procedure requires; we made our verbal Runway 11 verified" callout. We held short for a moment waiting for Tower to clear us for takeoff; and shortly thereafter we received our takeoff clearance for Runway 11. As we got onto the runway; I saw the old runway markings that had been removed and with the way the ambient lighting was; I did not notice taxiway lights or yellow taxiway edge markings I just saw what looked like the runway centerline where the markings had actually been removed; and in that moment of confirmation bias it looked like the yellow taxiway lead-on line was just that and did not extend beyond the turn onto the runway. We began our takeoff roll from A2; and passing through 40 knots the system began calling out "ON TAXIWAY ON TAXIWAY" approximately 200 feet from the Runway 11 threshold markings. By the time I registered the callout; I knew we were on the runway and called out "continue." It quickly became apparent in my mind that it was not a displaced threshold; but must have been a taxiway leading up to the threshold of Runway 11 as I now understand the FAA designates as an "aligned taxiway."After the flight; I began digging through the airport 10-9 taxi diagram; the 10-9A airport info; the 10-7/10-7A airport info pages; looked further at the FAA's Airport and Facility/Directory (AFD); and double-checked the NOTAMs to make sure I had not missed any kind of information that would allude to an aligned taxiway prior to the actual beginning of Runway 11. There was zero information about this aligned taxiway aside from taking a much more careful look at the AMM and 10-9 airport diagram charts. The only information that I found was online.This document outlines that new construction is being accomplished for a new runway being built 600 feet north of the current Runway 11/29. My assumption is that the runway is shortened in preparation for construction equipment working around and behind the new runway threshold and likely is to mitigate jet blast behind that portion of the old runway. On this link it specifies the following: "Note: The new threshold is east of the intersection of Taxiway A2 and Runway 11. Aircraft will taxi a short distance along the old Runway 11 to the threshold. The Grand Junction Airport Authority has specified that departing aircraft are not to use the old Runway 11 surface; west of the new threshold; for takeoff procedures."I began looking at historical ADS-B data on a website; and I found that 100% of the aircraft that I looked at departing Runway 11 were beginning their takeoff from A2 rather than rolling to the Runway 11 threshold at taxi speeds before applying takeoff thrust. I was able to notate that every single 121 airline operating out of GJT; as well as corporate jets; and military aircraft were all beginning their takeoff roll hitting the beginning of the actual Runway 11 at speeds between 40 and 60 knots ground speed. The ADS-B data specific to our flight shows us hitting the beginning of the actual Runway 11 at 53 knots ground speed. It is likely this issue has gone unnoticed or unreported.In summary; I do not think that this aligned taxiway has been properly addressed to provide information to all pilots during preflight planning for operating out of GJT off Runway 11; that there is in fact an aligned taxiway and not displaced threshold leading up to the threshold of Runway 11. Furthermore; getting this warning at such a critical phase of flight can be distracting and potentially lead to an inadvertent rejected takeoff; and pilots should be properly made aware of this potential threat at GJT."