If you have a completely sterile environment, a laminar flow hood, or are making large quantities for resale, then your logic might possibly hold true. For the average individual, making small quantities for personal use, then the caulking gun method is quick, simple, effective and easily addresses most safety concerns. This is coming from someone who has 2 autoclaves (one dry heat and one steam), an enclosed small laminar flow hood “clean room” and a size-able selection of filtration equipment and pumps, all for personal use.
In spite of having all of this available, due to me only producing about 36ml per batch, I find the caulking gun method much more convenient and practical. I am always testing different formulations, likely a couple per week, knowing I will likely only use a couple ml before placing the vials in my AAS storage bin.
Just because your personal preference is different for the filtering process does not mean that a different filtering process is trash.