"X and Y were in the garden, Y noticed the ripe tomatoes as they went into the greenhouse". Is X in the greenhouse?
I'm way woker than the average person but I have to admit encountering a singular 'they' breaks my concentration in a distracting way - there's definitely possible ambiguity.
People really ought to read redacted documents to get an idea for how people write with clarity when gender and even number of parties is unknown.
But I'm confused by your sentence regardless of the gender terms. Did they notice the tomatoes in the Garden or in the greenhouse? This is just ambiguous wording in general.
- These are two different sentences, but they're separated with a comma. It should be a period, as it makes no grammatical sense with a comma unless you're trying to make it intentionally confusing.
- You would write "They both went into the greenhouse" if they both entered, or you would write "Y entered the greenhouse and noticed the ripe tomatoes."
- "Before entering the greenhouse, "Y"/"they both" noticed the ripe tomatoes in the Garden."
They also applies to objects (like it does), so here it could be the tomatoes that are going into the greenhouse.