Genealogics.org, which references ESNF 5:148, says that his mother was Elisabeth von Montfort, the third of the four wives of Johann [II] Truchseß von Waldburg zu Trauchburg (see
https://genealogics.org/getperson.php?personID=I00105310&tree=LEO)
I do not have access to ESNF (at least as long as libraries remain closed due to COVID), but I do have access to the three-volume Waldburg family genealogy: Joseph Vochezer, _Geschichte des fürstlichen Hauses Waldburg in Schwaben_ (Kempten: 1888-1907). Vochezer had access to all of the family's archives and also did considerable research in the state archives at Stuttgart and Ludwigsburg, and the book is mostly a lightly digested summary of all the documents he found.
Based on my reading of Vochezer, I have some doubts as to who the mother of Jakob was.
According to Vochezer, there is only a single document that references Johann's third wife Elisabeth von Montfort: on 26 April 1399 the abbey of Isny issued a receipt to Johann for 1,000 Pfund Heller to endow a mass for, among others, his late wife Elisabeth von Montfort, her death to be commemorated on 16 October (Vochezer, I: 475-476, at
https://archive.org/details/bub_gb_VdwSAAAAYAAJ/page/n475/mode/2up). So she died on a 16 October of some year between 1390 and 1398 (Johann's second wife, Catharina von Cilli / Katharina z Celje, is known from her epitaph to have died 17 July 1389).
The only other relevant document is a charter from 4 July 1399 in which Johann made testimentary provisions for his son Jacob, his daughter Walpurg, and his wife Ursula von Abensberg (Romberg, "Repertorium über die Pergamenturkunden im freiherrl. von Hornstein'schen Archiv zu Binningen, Bez.-Amts Konstanz," _Mittheilungen der badischen historischen Commission_, 4 (1885): 134-194, on p. 136, nr. 21, at
https://archive.org/stream/ZeitschriftFrDieGeschichteDesOberrheinsvolume38/ZGO38#page/n517/mode/2up, also referenced in Vochezer, I: 481, at
https://archive.org/details/bub_gb_VdwSAAAAYAAJ/page/n481/mode/2up). This is the first reference to Johann's fourth wife.
Given that the 4 July 1399 charter mentions a son Jakob at the same time that the fourth wife is named for the first time, it is entirely possible that Jacob was a product of an earlier marriage (Jakob's two younger brothers Georg and Ernst were still minors in 1424, as is apparent from the homage document of 5 April 1424 cited by Vochezer, I: 499, at
https://archive.org/details/bub_gb_VdwSAAAAYAAJ/page/n499/mode/2up. Thus, they were clearly the sons of Ursula von Abensberg, contrary to the ESNF and Genealogics.org reconstruction). However, there are three circumstantial lines of evidence that at least suggest some doubt on this.
1) At least in the reconstruction of ESNF and Genealogics.org, the second marriage (ca. 1436/37) of Jakob to Ursula Markgräfin von Baden-Hochberg would have been consanguineous in the third degree (Elisabeth of Montfort's parents are shown as Konrad Graf von Montfort in Bregenz and Agnes von Montfort; this same couple were the great-grandparents of Ursula von Baden-Hochberg - see
https://genealogics.org/pedigree.php?personID=I00105308&tree=LEO&parentset=0&display=standard&generations=5). There is, however, no record of a papal dispensation for such a marriage (I know too little about German church practice in the 15th century to know whether a dispensation would even have been possible for consanguinity in the 3rd, as opposed to the 4th, degree). It should be noted, though, that I have seen no evidence whatsoever, in either the Waldburg family history or the Montfort family history (J. N. v. Vanotti, _Geschichte der Grafen von Montfort und von Werdenberg_ (Belle-Vue bei Konstanz: 1845), at
https://books.google.com/books?id=mGcPAAAAQAAJ), for the parentage of Johann's third wife Elisabeth von Montfort, so it is possible that this reconstruction is incorrect and that Jakob Truchseß von Waldburg's marriage to Ursula von Baden-Hochberg might not have been consanguineous in a prohibited degree even if Elisabeth von Montfort was Jakob's mother.
2) Waldburg family chronicler Matthäus von Pappenheim, writing sometime before his death in 1541, asserted that Johann had no children with his third wife Elisabeth von Montfort (Matthäus von Pappenheim, _Chronik der Truchsessen von Waldburg_ (Memmingen: 1777-1785), I: 70, at
https://books.google.com/books?id=f4dOAAAAcAAJ). However, Matthäus mistakenly calls her Magdalena von Montfort. Moreover, he was demonstrably wrong in the next generation when he claimed that Jakob had no surviving children with his second wife Ursula von Baden-Hochberg (von Pappenheim, I: 76); contemporary documents clearly show that Jakob's surviving son Johann Truchseß von Waldburg was Ursula's child (see a 1452 property settlement cited in Vochezer, II: 58, at
https://archive.org/details/bub_gb_Dt0SAAAAYAAJ/page/n81/mode/2up, as well as a 1466 document in Staatsarchiv Nürnberg: Reichsstadt Nürnberg, Losungamt, 7-farbiges Alphabet, Urkunde 3207, digitized at
https://www.gda.bayern.de/findmitteldb/Archivalie/387427/).
3) The only known daughter of Jakob was named Ursula (
https://genealogics.org/getperson.php?personID=I00105310&tree=LEO), suggesting a special relationship with his father's fourth wife Ursula von Abensberg. However, given the fragmentary nature of surviving documents, it is possible that Jakob might have had an earlier daughter Elisabeth who left no trace in the record.
Thus, it appears to me that there is no firm documentation for asserting that either Elisabeth von Montfort or Ursula von Abensberg was Jakob's mother - there is circumstantial evidence pointing in both directions, but nothing firm. To me the best solution (unless ESNF had access to evidence not available to Vochezer) seems to be that adopted by Cawley at Medieval Lands, to show Jakob as a son of Johann's [third/fourth] wife (
https://fmg.ac/Projects/MedLands/WURTTEMBERG.htm#JohannIIWaldburgdied1424B)