The very short answer to this is that they didn’t want to get into a war with the Slovenes.

The long answer needs to explore why that was, given that this question is one that was a big discussion twice during the Ten Day War - once at its onset and once around the time of the fiercest fighting in the Krakovo forest. Ultimately, the note at the end of your question is correct - if Yugoslavia really wanted to go all out in keeping Slovenia, they absolutely could have so, perhaps the question should be remodelled a little from “Why did Yugoslavia let Slovenia go?” to “Why didn’t Yugoslavia want to keep Slovenia?” to which there’s a few different answers

The first is ethnic - while this is a slight generalisation, the experience of the two republics to gain independence in a peaceful manner (Slovenia and Macedonia) is related to the fact that those two republics were also the most ethnically homogenous. There was no toehold for Serbs in Slovenia as there was in Croatia via the Krajina so there wasn’t as much clamour for the Serb majority JNA to be knocking heads together. If you consider the close of Yugoslavia as part led by Serb pressure to redefine it as Greater Serbia, it’s worth noting that there just aren’t really many models of a Greater Serbia that would actually stretch up as far north as the southern borders of Slovenia. The likes of Milosevic etc didn’t really have any specific territorial claims they wished to press on Slovenia. So in spite of Slovenia being the most affluent republic of Yugoslavia, it wasn’t one that the other side of the arguments around independence further to the south actually had much interest in.

The second is the nature of Slovenia’s departure. Whereas Croatia went from silent to seditious quickly, Slovenia’s departure was long in the making and, on top of that, Slovenia’s drive for independence wasn’t necessarily led by personalities that delighted in aggravating Yugoslavia (unlike Tudjman). The Slovenian independence movement (ie DEMOS) was led by a common cause across the political spectrum that saw multiple political parties with common cause tired with the direction in which Yugoslavia was travelling (unlike Croatia where it was more one party in the HDZ and everyone across the spectrum had to fit in it). While this isn’t intended to be a “why did Slovenia go” answer, it’s important to recognise their path out of Yugoslavia was likely set as far back as 1988 and the fallout from the JBTZ trial - they had time to plan.

Thirdly, and as a direct follow up to that, Slovenia wasn’t disarmed. While Croatia was disarmed in sometimes spectacular fashion, Slovenia were able to set up the MSNZ basically under the nose of the JNA and, in doing so, had a small armed force ready to go on day one. Being set on going for longer allowed Slovenia to plan for it and do things that others couldn’t.

Finally, there is of course the execution of the war itself. Slovenia isn’t really a great place to try and invade from the South even if you’re looking at a road map today - you’re generally kept to certain large routes (as near enough everything goes through Ljubljana), the further north and west you go, the more those routes are essentially just valleys and most of the nation is wooded. Aerial bombardment didn’t work (as Slovenia had good anti-air and helicopter arms and one of the first aerial missions killed foreign journalists) and the terrain just wasn’t helpful for shifting large volumes of troops and vehicles through.

If you have a small, mobile force that’s armed with the sort of stuff to take out tanks (which Slovenia’s military was), then you have the advantage in that terrain because the invaders have to take predictable routes and ambushes are really easy to set up. This is particularly the case when the ground work of not being disarmed meant that Slovenian forces didn’t really have to expend any manpower in taking control of much of the infrastructure, they just had to have soldiers remember to turn up to work in a different uniform to the day before independence, particularly when it came to border posts. So, by the time the JNA moved into Slovenia, they were met with an effective, well-organised force who had been planning a defensive war for some time and had blocked roads, etc so as to slow progress. The JNA had assumed that Slovene forces would just melt away but, instead, it was the JNA forces that deserted (a common theme through this and the Croatian War).

This turns to the point at the start of this response - there were two points at which a fuller invasion was contemplated, at the start and just before the conclusion (pushed hard by defence minister Kadijevic and JNA head Adzic). It would be fair to describe the JNA as overconfident at the start of the war and the assurances that Slovenia would be quickly brought to heel were enough to make the invasion limited. After the Ten Day War began disastrously thanks to Slovenia’s planning and their being able to isolate the JNA forces already in the nation from any reinforcements coming from the south, that question was revisited and political ambivalence won the day, especially given that matters in the Krajina were more pressing.

Had Slovenia not been as well prepared for invasion as they were or, for that matter, had the JNA had greater morale (or the extremely committed volunteer forces we see in Croatia) or had Milosevic been less ambivalent about Slovenia’s departure, then things would have certainly tipped a different way. As it was, the signature of the Brioni agreement (which essentially wrapped up Slovenia’s independence while driving a wedge between them and Croatia) was more politically expedient than actually carrying on with a war as long as Slovenia were able to accept that independence may mean they end up with a Greater Serbia at their border.