For many years your window panes would have been sealed in their frames with a two part butyl putty, sometime known as Marine Seal 033. We used this up until about 2017.
Marine Seal came in two large tubs (50Kg), one part black the other a cream colour. You mixed them together to create a black putty which could then be applied with a putty knife or similar after first applying the liquid primer. The putty (not unlike linseed oil putty used on timber house windows) took two weeks to cure, so there was plenty of time to re-smooth, a fact which made it suitable for DIY application (we used to sell kits and these were featured in a PBO article some years ago).
In contrast, Silicone does not require a primer or mixing but does require the bonding surfaces to be ABSOLUTELY clean and degreased with Acetone. Silicone goes off far quicker and you can't smooth or add more later (as new won't adhere to old).
Which is better?
Marine Seal shrinks and hardens with age and you end up with lots of narrow cracks across exposed surfaces. As it ages it begins to look more like a preformed rubber seal and indeed is easy to mistake for such. But as it shrinks it will become detached from one if not both surfaces and allow water in. This water may sit under the glass or come through to a second channel before staining your woodwork. We often find frames with solid salt deposits in the bottom of the lower channel.
Silicones do vary. Some have excellent adhesion to glass but none on Acrylic and the other way round, so be carful if thinking any will do. However, when the correct silicone product is used the result is a better bond and more more flexible and longer lasting seal. So we believe the correct silicone is better, much better. But, because getting the application right first time is critical, we view this as a workshop, not DIY job.
Don't some prefer Butyl?
I'm aware there are some 'professionals' who prefer Butyl, but I suspect this preference is more to do with the way they operate, often from a van. Cleaning surfaces is crucial for silicone to adhere and this is just not possible outside a workshop environment. Butyl is more forgiving for in-situ repairs, but only if you must.
But what about the articles in PBO about people refurbing windows?
Yes, there have been a number of articles in PBO recently where refurbishing windows for project and other boats has been discussed. Reading these you may note how crucial information is missing. The last talked about using 'mastic' to reseal. What is this, SPECIFICALLY. Butyl, Silicone, ARBOmast BR (Bedding compound, not for any glazing) etc etc. And what about the cleaning and then how do you achieve a nice smooth fillet? Sorry, but while written with the best intentions the devil is in the detail and more often than not this is missing....