The xls file format stopped being used natively in Office 2007. After that, you you have to make a conscious decision to use it , ignore the nag dialogue, etc.
You're assuming that Office is the only software to use XLS - it gets used a lot by other software, as a convenient and widely-supported interchange format. And if you believe the comments on the Reg article, that's what happened here - they suggest that PHE were collating data coming in from the various labs and then having to downgrade to XLS because it was the only format supported by a custom system inside the Track & Trace organisation.
Obviously that's only hearsay, but it suggests the issues were not with lab rats or PHE, but with T&T, which we know was not exactly the most sophisticated organisation. Those same comments suggest that NHSX, the NHS digital people who do generally know their stuff, were warning about this at a high level but because it was within T&T they didn't have any authority to change it.
Also the normal EOL dates don't really apply to the likes of the NHS, for instance in 2014
they paid Microsoft for XP support beyond the plebs' EOL date, because 85% of NHS computers were still running XP in 2013. And even in 2016,
90% of trusts that responded to a FOI still had some XP machines.
Although not relevant here, one issue is health-critical kit only being certified with particular combinations of hardware/software so you can't upgrade it without recertification (for which there's no budget).
In IT 's**t' doesn't just happen any more than it does in a lab. Poor decisions are made, often by smart people who think they know loads about IT because they can use mathlab or something and are a bit of a brain.
I think you're giving them a lot more credit for having a decision-making process than you should. And actually IME the people who use Mathlab etc are rather more aware of the limitations, the problems tend to be more in management who love Excel and don't really understand other options. Again, that sounds closer to what happened here.
Finally, the 'look they were busy dealing with a Pandemic' excuse doesn't wash. In logistics, we have put in robust systems and designed previously non-existant supply chains with proper IT to distribute all sorts of things around the pandemic, and we didn't feel the need to spin up some nonsense solution using Excel.
Logistics has a very different culture though - you're middlemen, so your IT is all about talking to other systems, whereas in the medical world, there's an element of making it difficult for systems to talk to each other, which originates in the culture of medical privacy but which goes rather beyond that in the real world. Don't forget that
it's only last year that the NHS was told it had to stop buying fax machines. Couple that with Treasury rules on capex, and a sprawling federal structure...it's a long way from how things work inside a corporate.
I'm not defending any of this, it's a long way from how things "should" be, but that's how it is. And that's the NHS/PHE which is the relatively competent half of this equation, I don't think anyone has much of a good word to say about the T&T mob.