I formerly studies chinese(simplified) for 10 years as my mother tongue and speak cantonese at home. As i still don't know the actual reading of the kanji in japanese, when i encounter kanji(mostly in light novel's title or chapter names), i just read out the hiragana and kanji in my head as chinese. I just automatically perceive kanjis in their chinese meanings first, if i encounter any, i just cant seem to stop this habit.

For those kanjis that i have never seen before in my studies of chinese, i translate them to english and try to put them into a sentence with some grammer i know.

I wonder if this will be a barrier to learning the readings in the future? Also slightly confusing for me are some japanese kanji with similar writings to traditional/simplified chinese but with different meanings all together.

On the other side of the coin, chinese also helped me skip some kanjis because i know of their meanings in chinese, and they mean the same. This is the good part i guess.

I study both chinese and japanese formally. And by myself (mostly japanese). It does happen a lot of times to me when I'm reading in chinese or ankiing chinese to read hanzi with japanese readings.

I don't know if anyone can say anything for sure, but my guess is that reading kanji as Chinese when you do not yet know their Japanese reading will probably not cause any long term problems, but it's probably not a good habit and probably won't do you much good either.
I think you should make an effort to learn their Japanese readings as soon as possible and pronounce them in Japanese in your head when you are reading.

I learned Japanese first and am now studying Chinese and when I come across a character I can't read yet in Chinese, I just gloss over it without pronouncing anything in my head, even if I know the word in Japanese. I also try to learn the Chinese pronunciation as soon as I can so that reencountering the character will reinforce its pronunciation.