I’m not sure what youre asking - you ask if they swap but mention multiple times “taller”, what does “taller” mean to you?
The struts don’t change the car height, so I’m not sure where you’re seeing they’re taller or why it matters - once installed there is no appreciable difference. Most people swap struts and keep the original springs. Use 00-04 springs on 00-04 outbacks and 05-09 springs on 05-09 outbacks. Use 00-04 struts on 00-09 outbacks.
if you want to worry about “height” then the discussion is about springs - most people install turbo baja springs in 00-09 outback at get a stiffer rear and extra 1”+ bump for loads/towing. Anyway height is about springs, not struts....you’re asking about struts but talking about height
I already said all this but 00-04 and 05-09 Outback struts are interchangeable. It’s very well known across Subaru world - as I already said people install 00-04 all the time in 05-09s, it’s almost a standard “upgrade” in DIY Subaru circles.
If you do go OEM, the OEM 00-04 struts are good struts.