The original game uses hardcoded paths for places where they cross over. You can hex edit the data for them to change them, though.
Code;------------------------------------------------
; hardcoded overworld path stuff
;------------------------------------------------
; list of level numbers with hardcoded paths
org $049078
; original values
; db $09,$15,$23,$1B,$43,$44,$24,$FF,$30,$31
; new values
db $09,$15,$23,$1B,$43,$44,$24,$FF,$30,$31
; X and Y coordinates for the position-based hardcoded path
org $049084
; original values
; dw $0178,$0128
; new values
dw $0178,$0128
; list of pseudo-Layer 1 tiles for hardcoded paths
org $049086
; original values
; db $10,$10,$1E,$19,$16,$66
; db $16,$19,$1E,$10,$10,$66
; db $04,$04,$04,$58
; db $04,$04,$04,$66
; db $04,$04,$04,$04,$04,$6A
; db $04,$04,$04,$04,$04,$66
; db $1E,$19,$06,$09,$0F,$20,$1A,$21,$1A,$14,$19,$18,$1F,$17,$82
; db $17,$1F,$18,$19,$14,$1A,$21,$1A,$20,$0F,$09,$06,$19,$1E,$66
; db $04,$04,$58
; db $04,$04,$5F
; new values
db $10,$10,$1E,$19,$16,$66,$16,$19
db $1E,$10,$10,$66,$04,$04,$04,$58
db $04,$04,$04,$66,$04,$04,$04,$04
db $04,$6A,$04,$04,$04,$04,$04,$66
db $1E,$19,$06,$09,$0F,$20,$1A,$21
db $1A,$14,$19,$18,$1F,$17,$82,$17
db $1F,$18,$19,$14,$1A,$21,$1A,$20
db $0F,$09,$06,$19,$1E,$66,$04,$04
db $58,$04,$04,$5F
; list of facing directions for tiles in hardcoded paths - 00 = up, 02 = down, 04 = left, 06 = right
org $0490CA
; original values
; db $02,$02,$02,$02,$06,$06
; db $04,$04,$00,$00,$00,$00
; db $04,$04,$04,$04
; db $06,$06,$06,$06
; db $06,$06,$06,$06,$06,$06
; db $04,$04,$04,$04,$04,$04
; db $02,$02,$06,$06,$00,$00,$00,$04,$00,$04,$04,$00,$04,$00,$04
; db $06,$02,$06,$02,$06,$06,$02,$06,$02,$02,$02,$04,$04,$00,$00
; db $06,$06,$06
; db $04,$04,$04
; new values
db $02,$02,$02,$02,$06,$06,$04,$04
db $00,$00,$00,$00,$04,$04,$04,$04
db $06,$06,$06,$06,$06,$06,$06,$06
db $06,$06,$04,$04,$04,$04,$04,$04
db $02,$02,$06,$06,$00,$00,$00,$04
db $00,$04,$04,$00,$04,$00,$04,$06
db $02,$06,$02,$06,$06,$02,$06,$02
db $02,$02,$04,$04,$00,$00,$06,$06
db $06,$04,$04,$04
; list of data indexes to the previous two tables
org $04910E
; original values
; db $00,$06,$0C,$10,$14,$1A,$20,$2F,$3E,$41
; new values
db $00,$06,$0C,$10,$14,$1A,$20,$2F,$3E,$41
. Progress: 64/95 levels.