Tough question! It really depends on your definition of better. If your definition is based on rigid compliance with standardized and validated processes and procedures with the accompanying extensive documentation, then you may conclude that cGMP manufactured peptide products are better than non-GMP grade peptides.
Another aspect of your definition of better would certainly include analytical testing, such as the number of tests, impurity limits, test result tolerances, and test methods. ACS Reagent products have no requirements for how a product is manufactured, only requirements for analytical methods and results. Unlike ACS Reagent chemicals, cGMP manufactured peptides may not have a compendium to be tested against (exception are generic peptides which are included in the US Pharmacopeia or European Pharmacopeia). As long as a manufacturer and their partner define the processes, properties, and results that are important to the partner, a cGMP manufactured product can have as many or as few analytical requirements as the partner deems necessary. cGMP peptide products must be manufactured using documented, validated processes. Any deviation from these processes can cause the product to be considered adulterated and potentially be rejected, even if it meets all of the analytical specifications.