It has to do with relationship. For example, Paul would say that certain people were in his heart, Jesus would say that the Father was in him and he was in the Father. The following is taken from Dake concerning the Luke 22:3 passage concerning interpenetration.If this is the case how does one explain how the "person" of the Holy Spirit is in all believers and exists everywhere??
[into Judas] Satan, as an angel, could not possibly enter physically into Judas, for he has his own personal spirit body as big as a man. The so-called doctrine of interpenetration, that is, persons entering physical into each other, is false. The Bible does speak of the Corinthians and Philippians being in Paul's heart (2Cor. 7:3; Php. 1:7); God being in Christ (2Cor. 5:19); Christ being in God (Jn. 14:20); God and Christ being in each other (Jn. 14:10-11); men being in both the Father and the Son (1Jn. 2:24); men being in Christ (2Cor. 5:17); men and the Spirit being in each other (Rom. 8:9); Christ being in men (Col. 1:27; Rom. 8:10); man and Christ being in each other (Jn. 14:20); all creation being in God (Acts 17:28); and Satan entering into men (Lk. 22:3; Jn. 13:27). However, these passages refer to being in union with, being consecrated to the same end -- one in mind, purpose, and life. They do not teach physical entrance of one being into another. It may be best understood by a man and woman becoming one in life together, being in each other's plans, life, etc. Hence, Satan entering into Judas simply means Judas submitted to Satan's temptation to betray Jesus. He became one with Satan, like men become one in spirit with God when joined to Him in consecration (1Cor. 6:17).
Dake's Annotated Reference Bible.