Your question seems to be: what is "fitness" used to mean? But you also seem to be misunderstanding what "bring [something] in line with [something]" means.
"To bring something/someone into line with something/someone else" is an idiom which means that the first thing is being raised to the standard of the second thing.
Cambridge Dictionary gives the definition as
to force someone or something to be similar or of the same standard as someone or something else
I think "force" might be too strong a word, as, in the case of your example, it can often be positive and nurturing rather than forceful.
coach Scott Pera tried to bring Harden's fitness in line with his talent and ambition
In your example, Harden already has high talent and ambition, and the coach is raising Harden's fitness to match them. The meaning of the sentence is that the coach is raising Harden's fitness so that it becomes of as high a quality as his already impressive talent and ambition.
In this case, fitness is almost certainly referring to cardiorespiratory fitness. This is the most common meaning of the word especially in everyday speech, and in this case in particular is supported by a previous statement in your source article:
Growing up, Harden was a bit chubby and asthmatic
Being chubby and asthmatic will negatively impact cardiorespiratory fitness, but not necessarily strength.
"Fitness" on its own is usually used to mean cardiorespiratory fitness. In general English usage, an endurance runner would be the first thing someone would think of when "fitness" is mentioned.
It's more unusual, but not incorrect, to use "fitness" to refer to other physical capabilities. Strongmen and powerlifters could be considered fit even though they may not have good cardiovascular endurance. People who get around with their bodies and can perform hard physical work are often considered fit.
It is normally only in technical contexts that "fitness" is used to refer to "suitability to the environment". Like in evolutionary science, a fitter animal will have more offspring, and homo sapiens turned out to be fitter than most not because of physical capability but because of our intelligence. It's rare to see people use this meaning of the word in general English, although of course English also has the idiom "fit for the job" which means well-suited for the job.