I have noticed discrepancies in how native Mandarin speakers spell certain words in Pinyin reflecting differences in pronunciation, for instance, pángbiān vs. pángbian and zǎoshang vs. zǎoshàng. I've been told that these reflect differences across dialects. I even find these discrepancies across dictionaries, so I'm wondering if anyone knows of a source for standard Pinyin spellings.
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When the tone that's written doesn't match what tone you'd expect to see that indicates that the transcription is meant to match the pronunciation. For example, the book "Modern Chinese Grammar" by Claudia Ross and Jing-heng Sheng Ma writes third tones as second tones when tone sandhi occurs. Other references do not necessarily do this.
What is more consistently done is omitting the tone mark when that syllable loses its tone in common use. Here, you will run into differences between regions; for example in Taiwan Mandarin speakers often keep the tone on a word's second syllable whereas in mainland China Mandarin speakers more often omit that tone.
Considering that the point of Pinyin is to show the pronunciation, it makes sense to leave off tones that are not pronounced. As for "standard pinyin spelling", looking up an individual character should give you its pronunciations with tone(s).
Note that sometimes the transcription reflects the actual reading rather than the "single-character-pinyin".
For example, 你好 is sometimes transcribed as ní hăo, even if the "actual" transcription per-character would actually be nǐ hăo. This happens because when two third tones are next to each other, the first one becomes a second tone (when reading/pronouncing the characters, not when writing).
In other cases there is a totall loss of the tone, such as in 窗户 (window) transcribed — and read — as chuāng hu1, rather than chuāng hù.
1: The source is the CEDICT dictionary.