Your alternative, with the comma
- This paper introduces a new alternative for generating synthetic data, which is based on images.
uses the non-defining relative convention
- John is my pen-friend, who lives in Canada. = John is my pen-friend; he lives in Canada.
as opposed to the defining convention
- John is my pen-friend who lives in Canada. = John is the pen-friend of mine who lives in Canada (not the ones in France, Tibet ...).
However, there is intrinsically still the ambiguity over whether this means that 'a new alternative for generating synthetic data' or 'synthetic data' itself is based on images. While this ambiguity is doubtless obviously resolved by logic in this case by most educated readers, the ambiguity 'which preceding noun phrase does the relative clause refer to?' is quite common and sometimes confusing.
Your relative clause if written without the comma would be defining, but must now really mean 'for generating image-based synthetic data'.
The original 'reduced relative clause' (some analysts disagree with the name/analysis) is interestingly ambiguous, either defining referring to 'synthetic data' (' ... image-based synthetic data') or non-defining referring to 'a new alternative for generating synthetic data'. The comma convention weakens with trickier examples. Reading these out, stress patterns would disambiguate: 'synthetic data based on images' read without a pause or stress on 'based on images' forces the defining sense (= ' ... image-based synthetic data'), with 'synthetic data' the modified NP. Stressing 'based on images' after a pause switches the meaning to [this new alternative is, incidentally, based on images']. But speech is more flexible than printed material.