Why is the Linking Melbourne Authority inflicting a high impact flyover on Clifton Hill and Collingwood?

Clifton Hill Interchange Map From Comprehensive Impact Assessment
Mapbook pp.19-35 (PDF 18MB) http://www.linkingmelbourne.vic.gov.au/pages/rosetta-download-pages.asp?file=cis-east-west-link–eastern-section-mapbook-1935.pdf 

The flyover was not required in an earlier design.

Clifton Hill Interchange Option, VicRoads 1999
Tunnel Report Part 4
http://ycat.org.au/NCCCS/Tunnel%20report%20part%204.pdf

“At Eastern FreewayThe primary objective of this interchange is to provide direct, freeway-to-freeway standard
connection to the proposed tunnel. Full connections to Hoddle Street are to remain. Options to reduce the number of lanes between Alexandra Parade and the Eastern Freeway can be investigated, depending of the extent of works proposed to aid access between the Eastern Freeway and the CBD. Options for deep and shallow tunnels have been investigated.

The option that appears to have the greatest potential has tunnelling commencing between Alexandra Parade and the railway bridge with split portals for the entry / exit tunnels west of Hoddle Street. The tunnel heads mainly in a westerly direction. This concept provides entry/exit access in a west / east direction respectively from the Freeway as well entry/ exit at Hoddle Street. The major advantage of this option is that it provides for full interchange movements between Hoddle Street and the tunnel /Eastern Freeway as well a wide range of traffic movements / alterations on the exiting ramps and/or carriageways during the construction period. The main disadvantage is the requirement for land acquisition for the southern tunnel requirements.”  From VicRoads 1999 Study Tunnel Options provided to the NCCCS study.

The 1999 version has portals much closer to Hoddle Street. Three freeway lanes slopes down to the tunnel from the railway bridge.

It retains the loop from Hoddle Street onto the freeway, and utilises the land inside the loop that contains a row of early elms.

Update: FOI documents obtained by The Victorian Greens show this interchange design was still being considered in 2012.
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