Those rocks should be fine! But you might wanna be careful as they get older, the General rule of thumb is that they'll try to swallow anything smaller than their head, haha
Sand is always a good option as well!
Flora base is not to be used as a substrate on it's own. Its designed to be placed under a layer of sand or gravel substrate giving plants a mineral rich and organic substance to feed of and take root in.
Flora base has been mentioned on the Axolotl Sanctuary article (Axolotl Sanctuary) as being Axolotl safe, but I have read many accounts of other fish keepers using the substrate saying that it will only last a year or so until the substrate turns to a thick muddy mess under the substrate, these specially formulated substrates are designed to be replaced every so many years as they break down into a messy consistency and eventually hold no minerals or organic matter.
If you are going to use Flora base, you should use a good inch of sand substrate on top since gravel can cause impaction.
I would remove the small pebbles you have in your tank, as your Axolotl grows these pebbles are small enough to be ingested. Purchase some that are a lot larger like these:
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