But by ordinary synthetic chemistry standards this represents a pathologically low concentration of material and the synthesis and storage of MBBs is almost certainly going to occur at quite higher concentrations, very likely in the mM range. But in turn this then means, if the MBBs have the same potential reactivity all the time, that the rate of random reactions jumps by a similar factor, namely about thousandfold. And so the raw materials would get degraded at an uncomfortably high rate by mere storage, before they ever even get to the scene of action. Clearly, this problem has to be addressed. Several potential solutions are thinkable.
Besides techniques like cryogenic storage and storage in an inactive or protected form, the presumably simplest method is the storage of only compatible classes of chemical polarities.
As the stability problem in storage arises mainly because MBBs will in the usual case have link-formation functionalities of both polarities (as e.g. amino acids do too), which enables them to react with each other and polymerize spontaneously, the problem could be solved by somewhat restricting the freedom of functionalization patterns. MBBs could be separated into different distinct classes of linking-chemistries, which contain functional groups of only one type of polarity that is not able to dimerize. This segregation of MBBs into classes of mutually compatible chemical polarities will limit the flexibility of inverting the polarity of links and produces more complicated constraints for designing and assembling macromolecules. But the big benefit will be on the practical side with much easier handling of the raw materials. Essentially no special precautions would have to be followed.