1200 years ago Kyoto was a small village. Not it is 3 million city with lots of concrete and asphalt. Cities are usually hot spots unlike small villages.
Cherry trees all across Japan (not just Kyoto) are blooming earlier and earlier
and this confirms that the trend cannot be explained by local urbanization alone c(https://gizmodo.com/japan-hasnt-seen-cherry-blossoms-this-ea...). However, Kyoto's transformation into a dense urban environment has for sure made the local signal worse.
same goes for famous Prague weather station Klementinum, now in concrete heat island obviously with higher average temperatures, they use to show long term trends
these comparisons are meaningless, you really need weather station in middle of nowhere (in nature away from people) for hundreds of years to get accurate readings for comparison