Good layout of 3d point data for spatial queries in Postgres?
The composite type is clean design, but it does not help performance at all.
First of all, float translates to float8 a.k.a. double precision in Postgres. You are building on a misunderstanding.
The real data type occupies 4 byte (not 8). It has to be aligned at multiples of 4 bytes.
Measure actual sizes with pg_column_size().
SQL Fiddle demonstrating actual sizes.
The composite type real3d occupies 36 bytes. That's:
23 byte tuple header
1 byte padding
4 bytes real x
4 bytes real y
4 bytes real z
---
36 bytes

If you embed that into a table, padding may have to be added. On the other hand the header of the type can be 3 byte smaller on disk. Representation on disk is typically a bit smaller than in RAM. Doesn't make a lot of difference.
More:

Configuring PostgreSQL for read performance
Calculating and saving space in PostgreSQL

Table layout
Use this equivalent design to reduce row size substantially:
    Column     |           Type           |                       Modifiers
---------------+--------------------------+---------------------------------
 id            | bigint                   | not null default nextval(...
 creation_time | timestamp with time zone | not null default now()
 edition_time  | timestamp with time zone | not null default now()
 user_id       | integer                  | not null
 project_id    | integer                  | not null
 location_x    | real                     | not null
 location_y    | real                     | not null
 location_z    | real                     | not null
 radius        | real                     | not null default 0
 skeleton_id   | integer                  | not null
 confidence    | smallint                 | not null default 5
 parent_id     | bigint                   |
 editor_id     | integer                  |

Test before and after to verify my claim:
SELECT pg_relation_size('treenode') As table_size;

SELECT avg(pg_column_size(t) AS avg_row_size
FROM   treenode t;

More details:

Measure the size of a PostgreSQL table row