They get used interchangeably and they are not the same thing. Each is derived differently, and one of them is not on a clock at all.
A muhurat is a named window judged suitable for something, the day or the night divided into fifteen parts, or a window defined by a tithi–nakshatra–weekday combination. A choghadiya is a running eight-fold division of the daylight, and again of the night, with a fixed cycle of seven names. Rahu kaal is a single one-eighth slice of daylight, picked by weekday.
What they share is that none of them is a fixed clock time. All three are cut out of the interval between sunrise and sunset, which changes with your date and your latitude. A rahu kaal quoted as "4:30 to 6:00, always" is describing one place in one season.
ZindSa divides sunrise-to-sunset into eight equal parts, and sunset-to-next-sunrise into eight more. Each slot carries one of seven names in a fixed repeating cycle, Udveg, Chal, Labh, Amrit, Kaal, Shubh, Rog. The cycle order never changes. The only thing the weekday changes is which name the first slot of the day starts on, and separately which one the first slot of the night starts on.
That is the whole mechanism, and it is why choghadiya is so easy to compute offline: it needs sunrise and sunset and nothing else. ZindSa marks Amrit, Shubh and Labh as auspicious and Chal as ordinary. The remaining three it does not label as bad. The app has a written tone rule against calling any time "inauspicious", the good windows are highlighted, and the rest are shown as ordinary or as time for rest.
Take the length of the day, sunrise to sunset, and divide it by eight. Rahu kaal is one of those eight parts, and which one depends only on the weekday. Gulika kaal and yamaganda kaal are derived exactly the same way from two other weekday tables. That is all there is to it arithmetically.
Two consequences follow. First, the duration is not fixed: in a short winter day each eighth is well under ninety minutes, and in a long summer day it is well over. Second, it moves with your location, because sunrise and sunset do. A printed rahu kaal table from another city is not your rahu kaal.
The muhurats ZindSa computes are shown with a label saying where each one comes from, derived directly from sunrise/sunset, or a widely-used panchang convention whose source verse the app has not itself verified, or a case where panchangs genuinely disagree. That label is on the card, not buried.
Brahma Muhurat is taken as 96 to 48 minutes before sunrise, and the app notes that some panchangs instead take the fourteenth of the night's fifteen muhurats, which shifts it. Abhijit is the eighth of the day's fifteen muhurats, so it is centred on solar noon and stretches or shrinks with the day, and the app records that the tradition of skipping it on a Wednesday is a rule whose source verse it has not verified. Godhuli is taken as twelve minutes either side of sunset, with the divergence noted. Nishita is the eighth of the night's fifteen. Amrit Siddhi Yoga is not a clock division at all: it occurs when the weekday's own paired nakshatra is running, so its window is the nakshatra's window.
Several muhurats and yogas you will find in other panchangs are deliberately absent here: Vijaya, Dur Muhurat, Amrit Kaal, Varjyam, Sarvartha Siddhi, Ravi, Dwipushkar and Tripushkar. They are missing for one reason, each depends on a table the project could not verify against a text.
The app's own note on that decision is blunt: attaching a warning flag to a wrong number does not make the number right. So they are not shipped with a caveat; they are not shipped. If and when the tables are confirmed, they arrive. Until then a gap is the honest output.
Related: the five angs of the panchang, and how the panchang is computed in the FAQ. All posts.