It does not matter. For two reasons.
PHP is a script language
So if the performance is important, the language is wrong. You'll have an unbelievably greater gain than worry about it. As Donald Knuth says:
We should forget about small efficiencies, say about 97% of the time: premature optimization is the root of all evil
We must forget small inefficiencies in 97% of the time: premature optimization is the root of all evil.
This is a classic case that the rest around it consumes much more time and this will not make significant difference. Especially in a Singleton that will not run multiple times (and I did not even merit that Singleton in PHP is a cannon to kill bird, that is, creating a simpler architecture will give a much better performance than worry about it). PHP is extremely inefficient.
And I've seen PHP have absurd performance differences from one version to another, and without criteria, so what may be valid one day may not be in the other.
They did a test , but I relied on a post because I know how the human brain works and will consider it useful , when in fact it is not. Note that it uses an old version, we do not know the exact conditions and it was very badly measured since the cost of starting and stopping the clock so many times must be interfering much more in the result. Almost all of the benchmark tests I've seen being done in PHP are wrong.
Different semantics
The second reason is that they do very different things. Almost always cloning something is a mistake and has implications that few people dominate. There is a specific semantics of how the object will be copied which is not always obvious. So creating a new object the way you're looking at it in code is often the solution. The biggest problem with cloning something, and even knowing which is the slowest, is because maybe it does things you do not even expect it to do, and we would be comparing apples to oranges.
In fact, even this can become a problem. Not to mention that having these objects can be an unnecessary complication, but this is another matter.
It's even complicated to measure accurately in PHP, and the results are often inconsistent and measure things other than this particular point.
And there is a wrong premise in the question. The clone
"redo" instance yes. It creates a new object and makes a copy.
Your Low-Performance Case
Most likely bad performance comes from another point and motive. Just start thinking about improving something's performance when you can prove it's what's causing the loss.
Again, simplify your code and architecture, understand what you are doing, and measure properly. If none of these solve, and should, change language there. But changing the language and not solving these other problems will help very little.
Test PHP with faster language. If the test is done properly in the right things you will see an absurd difference. Although PHP addresses certain issues, when performance is the most important, it is inadequate, this is measurable, it is not a matter of opinion.