Khatzumoto recommended skimming mostly as a motivational tool. You skim boring parts to get to the fun parts, and it keeps you focused on your immersion.
When it comes to reading speed, skimming won't help. If you read a lot, your reading speed will improve naturally. To increase your reading speed you need to read at your natural speed, and read a lot. Slowly over time your natural reading speed will get better.
The more you read, the more your brain will be able to recognize patterns and
group words together. For example, when you first start learning Japanese, you
may need to read each character individually to understand long patterns
But as you become more familiar with the language,
you will be able to recognize longer patterns instantly,
without having to say each syllable in your head.
Your brain will become able to process multiple characters and multiple words as single units.
you start to chunk the language into larger and larger pieces.
As you become more accustomed to picking up groups of words as single units,
your reading speed increases due to the decreased number of chunks you have to process.
So the key to being able to read faster naturally is building the mental infrastructure in your brain. Forcing yourself to read faster than you are comfortable will not lead to the desired result. Speed is only achievable through dedicated practice and time.
I don't recommend skimming, as it can lead to missing important information. It is much more beneficial to be able to actually read and recognize each piece of the text, rather than just jumping through words, skipping chunks and inferring the meaning from the context. While it can be possible to comprehend and infer the meaning of Japanese text without certain parts, such as conjugations and particles, the lack of exposure to essential words and grammar may impede one's ability to use them when speaking. For language acquisition it is important that you pay attention to each bit of information in the text so that your brain can absorb the patterns and acquire grammar. Avoid skimming in order to gain maximum exposure to all elements of Japanese.