Well here's my advice. Start off with common sense, that's the starting point before being taken in by some 'experts' statement.
Common sense says there is a natural reason for stretching. Look around you and you will see people, animals etc. stretching naturally. Look at yoga and ballet and areas where it's already down to a fine art.
Then you will see there is nothing wrong and in fact there is something right about stretching. Then you have a good base from which to study what's being said rather than being a 'lemming'.
So actually it's a no brainer that stretching is good so the questions about it are not whether it is or not but rather when it is and why? Then move to how?
Unfortunately common sense can be an abyss to some
Next suwariwaza. Why? What does it do that's so special? What exactly are you exercising and learning? What's the basic reason?
Once again I find lack of understanding the reason for much discourse all off the point.
It is exercising a part that I have discovered on this board anyway in the past and also in my experience meeting all except for Japanese, a part that people have little reality on. This part is Koshi.
To most the only reality they have on Koshi is based on something given the name like koshiwaza. Thus they don't even know the significance of it and use of it other than for throwing over the hips. I am always amazed by this lack of knowledge.
Suwariwaza is actually learning to use koshi along with centre. It also results in great posture for koshi is the base of good posture, martially too. So you learn to experience koshi, use koshi, learn about koshi, move fluidly from koshi and if you are into the spiritual then join up the missing dots relating to such. Thus a basic. It's also the base of relaxation....koshi.
One third of Aikido. Many I've met... one third missing.
Now when it comes to knees, ahhhh, the old 'excuse'. Back to common sense. Common sense says here in the west and many places other than people are not used to their body being put in such a position. Even sitting seiza is uncomfortable. Well with seiza it's a matter of gradually stretching those tendons until it's no problem. But knees? There's a problem for they can be a bit delicate when not used to it. So actually it is something to give some consideration to but not to use as an excuse. The solution is actually very simple and again common sense.
Get the knees used to it, comfortable with it, acclimatized to it, happy with it. How? By using thicker and thus softer mats ie: more springy. The knees love it. Then meanwhile the ligaments and all parts used get used to it and build up appropriately. The rest is based purely on learning to move from centre and the balancing of use of koshi whilst moving.
Enjoy the abyss.