Argument from Authority is generally fallacious if used on its own. But reliance on authorities can sometimes be justified in conjunction with other evidence, which aims to demonstrate that there is more objective evidence for the conclusion than against it, that the experts have considered both sides, that the experts are competent, free, and motivated to recognise bad evidence and reject it, and that there are no factors at work preventing experts who disagree with the consensus from being heard and considered.
You deduce the existence of sufficient subject-relevant evidence by arguing that the experts will have checked for it and would behave differently if it didn't exist.
So for your example of a software tool, you would want to know whether the programmers you're talking about have checked out a range of tools, are competent and motivated to evaluate them fairly, are not constrained by commercial or contractual interests, differential availability or awareness, advertising, educational background, etc. and whether individuals producing better tools will be recognised and adopted.
So there are some software products that are widely used simply because they are widely available. UNIX was offered for free to universities, when other operating systems cost money. So everyone learned UNIX at college. Microsoft Windows and Explorer were distributed at no extra cost on PCs, so many people never bothered to download or buy alternatives. People in big companies often use Microsoft Excel for doing bulk statistical data analysis, because the companies often did a deal to install Microsoft Office on every machine, so it's already there, available, and familiar to the users. If several of the biggest software developers adopt a particular suite, programmers hoping to work there, or who previously worked there, are all familiar with it. Or software may be kept long after something better has been created because of the investment in all the legacy code built up reliant on the old tool, that would have to be binned and rebuilt at great expense.
Just because they're widely used doesn't mean they're the best for the job. Programmers under pressure tend to start with the languages, technologies, and applications they're familiar with, and only explore other options if the difficulties of using their default option are insurmountable. Not always, but often enough.
It is also often not clear whether the criteria for 'best' are widely agreed upon. Programmers very often argue about what language or operating system is better. And the continued existence of multiple solutions suggests it is not clear cut. Is Python better than C++? There is still lots of C++ code being developed, so clearly not everyone has decided that Python is superior and moved everything across. But if C++ was clearly better, why has Python appeared and taken off? Does this behaviour support the belief that programmers choose what tools to use based on objective and universally applicable criteria of quality/correctness?
Experts may be expert on one subject but not on a closely related subject. Experts may be out of date, or have expertise specific only to a particular locale. Experts may be paid to hold an opinion, or be so invested in one side of a controversy as the foundation of their career, reputation, and livelihood that they are not objective about it any more. And established experts in a field may have the power and influence to exclude people who disagree with them from being considered experts. An expert may have relied on Argument from Authority themselves and have learnt everything they know from uncritically accepting the pronouncements of other experts (like their university lecturers), same as you. Nobody has the time to examine the evidence for absolutely everything they believe and rely on. Experts are fallible, corruptible, sometimes lazy. Fundamentally, experts are only human.
Richard Feynman said "Science is the belief in the ignorance of experts." Assuming ignorance is the starting default position. Expert opinion can provide indirect evidence of correctness/quality, but you first need objective evidence that the experts are worth listening to! You can't just take it for granted because they're called 'experts' in their job title. But if there is evidence that the experts are diligently applying the scientific method - constantly challenging consensus and systematically seeking out other points of view - then expert opinion can provide an indirect source of evidence for the existence of justifying evidence on subjects too technical for the layman to examine the specific evidence directly.