Ther is no simple truth because thare are many variables to consider. Some samples are hard to lyse or disrupt so lead to low yields of dna or are contaminated with molecules that look like dna (soil samples have humins as a contaminant) and may need unusual disruption ( ball mills) or unusual chemistries (CTAB additive). All of the kits you mention are well tested and work but can suffer if overloaded or the membranes are not washed well and mostly suffer from low yields but are best for small amounts of dna.. Phenol chloroform is very good for large amounts of starting material and is applicable for a wide range of crude dna samples but some people dislike the safety aspects of working with phenol and there are storage issues with phenol which can lead to poor dna purification

In practice, the choice between these methods depends on multiple factors including the sample type, the scale of the operation, and the specific requirements of the SNP genotyping or sequencing platforms. For routine applications where safety, convenience, and efficiency are priorities, Qiagen’s kits are highly recommended. However, for projects demanding the utmost DNA purity or when handling complex samples, the phenol-chloroform extraction remains invaluable. To determine the most effective approach for your specific conditions, conducting small-scale trials with both methodologies may provide insightful comparisons, guiding you towards the optimal choice for achieving reliable and reproducible results.