The article itself answers the question, albeit not in the most direct way. It cites Law Commission (England & Wales) Report No LC245 (1997), which discusses the relevant law in significant depth in Part XIII: Computer Evidence. Additional discussion is contained in the preceding Consultation Paper No CP138 (available at the same link) at paragraphs 14.27–14.32.
In short, the presumption comes from the common law, and in particular Castle v Cross [1984] 1 WLR 1372, 1377B (Stephen Brown LJ). In Castle, the following extract from Phipson on Evidence was approved by the Divisional Court: "In the absence of evidence to the contrary, the courts will presume that mechanical instruments were in order at the material time" — M N Howard, P Crane and D A Hochberg (eds), Phipson on Evidence (14th ed, 1990). The Law Commission felt that this was the appropriate rule.
However, section 69 of the Police and Criminal Evidence Act 1984 (UK) ("PACE Act") had overridden the common law presumption in respect to computers. Under PACE Act s 69, the prosecution had to prove the computer was working properly. The Law Commission recommended repealing that and restoring the common law presumption. Hence, the Youth Justice and Criminal Evidence Act 1999 (UK) eventually repealed PACE Act s 69.
As a response to this reply notes, the repeal has attracted criticism. Christie asserts rather scathingly that "the Law Commission misunderstood, or misrepresented, the opinions of the sources cited as being in favour of repeal", failing to understand the problem and ignoring expert advice: James Christie, "The Law Commission and section 69 of the Police and Criminal Evidence Act 1984" (2023) 20 Digital Evidence and Electronic Law Review.