Depending on the development cycle of Chlamydia tend to appear in two forms, the elementary body and the reticulate body. As outlined in the excerpt below, the reticulate body can be found as inclusions in a cell's cytoplasm when stained with iodine. So yes, your initial guess of inclusion-forming units (IFUs) being a measurement of how much of Chlamydia spp is present in a sample (cell or tissue) is correct.
It is similar to the concept of Colony Forming Units (CFU) which is a unit used to estimate the number of viable bacteria or fungal cells in a sample. Viable is defined as the ability to multiply via binary fission ("division in half") under controlled conditions.
Applying the concept of CFU to the above an inclusion-forming unit may be understood as a unit to estimate the number of Chlamydia cells in a sample. The difference between CFU and IFU would be as follows, CFU counts are normally taken for bacteria/fungi grown in a controlled environment. CFU counts also only account for viable cells, dead cells are disregarded. This is in contrast to IFU counts as we do not have a controlled environment as such and depending on what staining method you use, IFU counts may or may not account for dead cells too.
Chlamydia may be found in the form of an elementary body and a reticulate body. The elementary body is the nonreplicating infectious particle that is released when infected cells rupture. It is responsible for the bacteria's ability to spread from person to person and is analogous to a spore. The elementary body may be 0.25 to 0.30 μm in diameter, and it mainly consists of C. trachomatis, C. pneumoniae, and C. psittaci. This form is covered by a rigid cell wall (hence the combining form chlamyd- in the genus name). The elementary body induces its own endocytosis upon exposure to target cells. One phagolysosome usually produces an estimated 100–1000 elementary bodies.
Chlamydia may also take the form of a reticulate body, which is in
fact an intracytoplasmic form, highly involved in the process of
replication and growth of these bacteria. The reticulate body is
slightly larger than the elementary body and may reach up to 0.6 μm in
diameter with a minimum of 0.5 μm. It does not present a cell wall.
When stained with iodine, reticulate bodies appear as inclusions in
the cell. The DNA genome, proteins, and ribosomes are retained in the
Link to Wikipedia page - excerpt was taken from there.