It can be set according to the convenience. I don't think it's a problem. I ranked my map in this format the other day. https://osu.ppy.sh/beatmapsets/2283085#osu/4873602
It isn't strictly a problem but it's something you can surely consider for your overall quality and consistency of hitsounds. You can simply copy normal-hitwhistle.wav as soft-hitwhistle.wav to resolve this.
Right now it is consistent only with the default skin because normal-hitwhistle.wav is a copy of the default soft-hitwhistle.wav making it indistinguishible. But it is distinguishible with skins that have custom soft-hitwhistle.wav. And many many players use custom skins.
Seems you could use a different soft-hitwhistle sound for the kiai section because you mainly use it for the instruments and not vocals like in non-kiai. I attached 2 example files:
soft-hitwhistle.wav - would recommend using this for all the vocals - it has a bit more feedback than the default whistle and doesn't blend in as much with soft hitnormalsoft-hitwhistle2.wav - would use this for instruments in kiai. Just note ofc you'd have to match the remaining sampleset. At some sections like 00:59:992 you could still switch back from custom 2 to 1 as the vocals are introduced again and the melodic instrument disappears.Note these are only examples, any alternatives in this direction are nice.