I don't think you are understanding correctly. Nobody is saying that "by" cannot mean "with." In fact I told somebody the other day in another forum that "by" and "with" can mean the same thing. The problem is that it's only ONE definition of "by" and "with" that are the same, not all. They are not always synonymous. What is being said is that "by" doesn't mean "with" in the sense of "accompanied with."
Were all things made accompanied with Jesus? Was Jesus just there with the one creating, or was Jesus Himself the one creating it? Obviously it is the latter.
I fully realize that the word "by" has several meanings. It is dwmoeller1 who said the word by (dia) never means "with" in the NT. Well, I think John 1:3 is an example of where his is in error, it absolutely means "with" in this verse, the word "without" making that obvious.
The issue we are debating is the use of "by" in Hebrews 9:12
Heb 9:12 Neither by the blood of goats and calves, but by his own blood he entered in once into the holy place, having obtained eternal redemption for us.
In Hebrews, Jesus is directly compared to the OT high priest who offered a blood sacrifice for the sins of the people. The high priest absolutely had to have this blood "with" him when he entered the holy place. But dwmoeller1 believes Jesus did not have to have this blood "with" him.
Why make the comparison then? It makes no sense. But there are several others verses that strongly imply he had this blood "with" him.
Heb 9:21 Moreover he sprinkled with blood both the tabernacle, and all the vessels of the ministry.
22 And almost all things are by the law purged with blood; and without shedding of blood is no remission.
23 It was therefore necessary that the patterns of things in the heavens should be purified with these; but the heavenly things themselves with better sacrifices than these.
24 For Christ is not entered into the holy places made with hands, which are the figures of the true; but into heaven itself, now to appear in the presence of God for us:
25 Nor yet that he should offer himself often, as the high priest entereth into the holy place every year with blood of others;
The OT high priest couldn't simply kill the sacrifice and pour it's blood on the ground, he had to enter the tabernacle and sprinkle the tabernacle and all the vessels (verse 21).
Again, why point this out if Christ did not have to do the same? If Christ did not have to sprinkle the tabernacle and the vessels, why mention it?
And why does it mention the high priest entering in the holy place with the blood of "others" (verse 25). This is a very strong implication that Jesus entered in with his "own" blood.
In chapter 8 it says that "every" high priest had to offer gifts. And then it says of "necessity" that Jesus "also" have somewhat to offer. Again, the high priest couldn't pour the blood for the sin offering for the people outside, he had to carry it into the holy place and sprinkle around and on the mercy seat. And I believe this strongly implies Jesus had to do the same.
Heb 8:3 For every high priest is ordained to offer gifts and sacrifices: wherefore it is of necessity that this man have somewhat also to offer.
Again, why go to the trouble to mention these obligations of the OT high priest to enter with blood and sprinkle the tabernacle and vessels if Jesus did not have to do so also? It doesn't make a bit of sense.