I think what Bruce Lee and those who have said similar things both before and after him are getting at is that it's a process, not a set product. Through this process, you take what seems to work "better" at the time you're testing it, and you discard the "worse" which came before.
At any point in that journey, you can never say you've found the ultimate set of techniques which are the best in absolute terms, because it necessarily depends on you as an individual and everything you've experienced prior to arriving at this point in time. And it's also because you're limited as a human being. You can't explore everything there is. Your knowledge will never be complete.
That's what Jeet Kune Do is supposed to be. It's a process. It's not a rigid set of techniques culled from Bruce Lee's investigation into martial arts. Or at least, it shouldn't be.
Bruce Lee famously began with Wing Chun kung-fu as his foundation, but gradually, as he learned more about other fighting styles, little by little he put each piece under the microscope and determined that there were better techniques and strategies for dealing with fighting in different scenarios. He held on to the last tiny pieces of Wing Chun until there was nothing left to hold. He simply found better answers than Wing Chun offered.
Wing Chun, on the other hand, was someone else's answer at some point in their martial arts journey. It was simply better than what came before.
Now on to your question about how this philosophy fits in with beginners and not just people who are already quite skilled. The answer is hopefully a little more clear now. To a beginner, everything seems better. They begin with whatever style they want. But if they apply the philosophy of Jeet Kune Do, they will grow beyond the bounds of that first style they learned.
Eventually, after a lot of experience and careful analysis, an individual who goes through this process may come to realize that there is no style which has all the answers and which is best at everything. Because after all, what is a style but a collection of techniques, ideas, and strategies that someone put together? We're all finite and therefore limited. So styles should also be limited.
As for MMA, it is perhaps the best example of Jeet Kune Do in practice today, albeit with a focus on sport instead of survival. Anyone who has watched it progress from UFC 1 to today has seen a real evolution at work. At first, anyone who knew ground fighting could win. Since then we've seen fighters being able to dominate using a striking style derived from traditional martial arts. We've seen the rise of wrestling's influence. We've seen boxing's influence. We've seen muay thai's influence. We've seen some Capoeira. We've seen San Da kung-fu. We've seen Judo. We've even seen some practical use of Taekwondo.
Each fighter is taking bits and pieces of other things they've learned and putting it to the test in MMA. Sometimes it catches on, and for a while everyone seems to go out and learn those techniques. It's because people see how it can give them an advantage in some circumstances.
What can we say about techniques in absolute terms? Must we always speak of a particular individual's use of the technique, rather than considering the merits of the technique on its own? In other words, can we say there are better techniques and worse techniques?
The answer is yes, we can say some techniques are better than others on their own merits, but let's qualify that.
We know from MMA that there are "low percentage" techniques. These are techniques that are seldomly used in MMA and do not score very reliably. But that in and of itself doesn't mean that they're inferior techniques. It could just mean that nobody is skilled enough in those techniques to be able to use them.
Yes and no. There are reasons why you don't see, for example, a lot of people doing the outer-wrist throw, and it's not because there are no former black belt Aikido practitioners doing MMA. There are. It's just that this particular technique first requires that you catch someone's hand while they aren't tensed up, while they aren't flailing said hand, and while they aren't doing something to you which requires your attention, all while letting you do the throw instead of attacking you or tensing up their arm. Needless to say, this is completely unrealistic and unlikely to occur in a real MMA fight.
But don't take my word or anyone's word for that matter. Put it to the test yourself. That's what Bruce Lee did. You have to actively try it on live, fully resisting opponents. The more the better. This is called "pressure testing". You'll learn quickly if it works or not.
There just aren't a lot of opportunities that come up in a fight whereby the outer-wrist throw can be used successfully.
Judo has something similar to say about this. The way Judo organizes its throws in terms of which ones you learn first is very practical. They teach the most effective throws first. What does that mean? Are some throws more powerful than others? No. That's not what they mean by "effective" in this case. Instead, they mean that the throws you learn first are the ones that apply in the most situations you'll encounter in real life. The throws you learn last will be throws that you can only use in special, less frequent circumstances.
In other words, it's about opportunity. Which is another way of saying probability.
So this all comes down to what is "probably" going to be the most effective way of spending our time, given that we all have a limited amount of time to live our lives. We will never know for certain what's best in absolute terms, but we can use our intuition, experience, and reasoning skills to determine what makes the most sense for our own selves at any given moment in our lives.
Hope that helps.